Starting phenix.real_space_refine on Thu Mar 5 00:44:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v02_26927/03_2026/7v02_26927_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v02_26927/03_2026/7v02_26927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v02_26927/03_2026/7v02_26927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v02_26927/03_2026/7v02_26927.map" model { file = "/net/cci-nas-00/data/ceres_data/7v02_26927/03_2026/7v02_26927_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v02_26927/03_2026/7v02_26927_neut.cif" } resolution = 4.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 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 29 5.49 5 S 49 5.16 5 C 10999 2.51 5 N 2928 2.21 5 O 3412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17417 Number of models: 1 Model: "" Number of chains: 9 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: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2354 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain breaks: 3 Chain: "F" Number of atoms: 5292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5292 Classifications: {'peptide': 650} Link IDs: {'PTRANS': 7, 'TRANS': 642} Chain breaks: 6 Chain: "G" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 624 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 10, 'rna3p': 18} Chain: "H" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2378 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 1 Chain: "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 Time building chain proxies: 3.99, per 1000 atoms: 0.23 Number of scatterers: 17417 At special positions: 0 Unit cell: (96.219, 119.739, 186.023, 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 49 16.00 P 29 15.00 O 3412 8.00 N 2928 7.00 C 10999 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 674.0 milliseconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3886 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 47.7% alpha, 15.7% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.695A pdb=" N ILE A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 178 removed outlier: 3.685A 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 Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 178 removed outlier: 3.564A pdb=" N ASN B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.558A pdb=" N ILE C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 3.687A pdb=" N HIS C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 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 'E' and resid 42 through 53 Processing helix chain 'E' and resid 55 through 65 Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 75 through 82 removed outlier: 3.670A 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: 3.679A pdb=" N ILE E 134 " --> pdb=" O PRO E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 156 removed outlier: 4.191A pdb=" N SER E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 211 through 230 Processing helix chain 'E' and resid 237 through 247 Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'E' and resid 278 through 290 Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 15 No H-bonds generated for 'chain 'F' and resid 13 through 15' Processing helix chain 'F' and resid 16 through 24 removed outlier: 3.872A pdb=" N ILE F 20 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY F 24 " --> pdb=" O ILE F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 42 Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.653A pdb=" N LEU F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 67 removed outlier: 4.096A pdb=" N LYS F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 152 through 170 removed outlier: 4.245A pdb=" N TYR F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 190 removed outlier: 3.900A pdb=" N GLN F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 227 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 239 through 249 Processing helix chain 'F' and resid 261 through 267 Processing helix chain 'F' and resid 273 through 300 removed outlier: 3.597A pdb=" N SER F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE F 283 " --> pdb=" O ARG F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 322 through 344 Processing helix chain 'F' and resid 358 through 363 removed outlier: 3.611A pdb=" N LEU F 362 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET F 363 " --> pdb=" O GLY F 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 358 through 363' Processing helix chain 'F' and resid 367 through 384 removed outlier: 3.774A pdb=" N THR F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 398 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 424 through 437 removed outlier: 4.530A 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 536 through 542 Processing helix chain 'F' and resid 550 through 573 removed outlier: 3.625A pdb=" N THR F 554 " --> pdb=" O SER F 550 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU F 569 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN F 570 " --> pdb=" O LYS F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 612 Processing helix chain 'F' and resid 630 through 638 removed outlier: 3.990A pdb=" N PHE F 636 " --> pdb=" O SER F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 670 Processing helix chain 'F' and resid 674 through 686 Processing helix chain 'F' and resid 690 through 703 removed outlier: 4.005A 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 120 Processing helix chain 'H' and resid 168 through 183 Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 231 through 236 Processing helix chain 'I' and resid 15 through 24 removed outlier: 3.907A pdb=" N GLU I 19 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 47 Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 92 through 102 Processing helix chain 'I' and resid 103 through 115 Processing helix chain 'I' and resid 116 through 137 Processing helix chain 'K' and resid 15 through 24 removed outlier: 5.084A pdb=" N VAL K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS K 22 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER K 23 " --> pdb=" O GLU K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 47 Processing helix chain 'K' and resid 48 through 65 Processing helix chain 'K' and resid 71 through 92 Processing helix chain 'K' and resid 92 through 102 Processing helix chain 'K' and resid 103 through 115 Processing helix chain 'K' and resid 116 through 137 removed outlier: 3.888A pdb=" N TYR K 137 " --> pdb=" O TYR K 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 103 removed outlier: 5.574A pdb=" N VAL A 151 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A 101 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASP A 149 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE A 103 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU A 147 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 9 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS A 4 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N THR A 201 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS A 6 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 199 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER A 8 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR A 197 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 124 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.511A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.472A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS B 4 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR B 201 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS B 6 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE B 199 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER B 8 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR B 197 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 127 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.571A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.571A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR C 10 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASP C 196 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU C 12 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE C 194 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 119 through 127 Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 160 Processing sheet with id=AB1, first strand: chain 'E' and resid 19 through 24 removed outlier: 4.938A pdb=" N GLN E 22 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 38 through 41 Processing sheet with id=AB3, first strand: chain 'E' and resid 184 through 193 removed outlier: 7.186A pdb=" N MET E 186 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASP E 178 " --> pdb=" O MET E 186 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU E 188 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLN E 175 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR E 315 " --> pdb=" O GLN E 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 307 through 311 removed outlier: 6.570A pdb=" N TYR F 316 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR F 310 " --> pdb=" O HIS F 314 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA F 315 " --> pdb=" O MET F 257 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 417 through 418 Processing sheet with id=AB6, first strand: chain 'F' and resid 450 through 452 removed outlier: 4.168A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 461 " --> pdb=" O PHE F 441 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE F 441 " --> pdb=" O ILE F 461 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE F 478 " --> pdb=" O THR F 492 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 578 through 584 removed outlier: 5.725A pdb=" N ALA F 580 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE F 591 " --> pdb=" O ALA F 580 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL F 528 " --> pdb=" O GLY F 623 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 63 through 65 removed outlier: 3.519A pdb=" N GLY H 160 " --> pdb=" O TYR H 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 58 through 59 Processing sheet with id=AC1, first strand: chain 'H' and resid 71 through 73 Processing sheet with id=AC2, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AC3, first strand: chain 'H' and resid 273 through 274 Processing sheet with id=AC4, first strand: chain 'H' and resid 243 through 246 removed outlier: 3.693A pdb=" N SER H 267 " --> pdb=" O THR H 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 283 through 284 Processing sheet with id=AC6, first strand: chain 'I' and resid 25 through 26 removed outlier: 3.552A pdb=" N LYS I 26 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL I 38 " --> pdb=" O LYS I 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 804 hydrogen bonds defined for protein. 2325 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5494 1.34 - 1.46: 4089 1.46 - 1.58: 8075 1.58 - 1.70: 57 1.70 - 1.82: 86 Bond restraints: 17801 Sorted by residual: bond pdb=" O3' U G 22 " pdb=" P A G 23 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.17e+01 bond pdb=" C3' U G 24 " pdb=" O3' U G 24 " ideal model delta sigma weight residual 1.417 1.466 -0.049 1.50e-02 4.44e+03 1.07e+01 bond pdb=" N ILE F 120 " pdb=" CA ILE F 120 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.04e+01 bond pdb=" N ILE A 91 " pdb=" CA ILE A 91 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.65e+00 bond pdb=" N ASP E 122 " pdb=" CA ASP E 122 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.14e-02 7.69e+03 9.46e+00 ... (remaining 17796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 23405 2.54 - 5.08: 580 5.08 - 7.61: 80 7.61 - 10.15: 10 10.15 - 12.69: 4 Bond angle restraints: 24079 Sorted by residual: angle pdb=" C4' A G 27 " pdb=" C3' A G 27 " pdb=" O3' A G 27 " ideal model delta sigma weight residual 109.40 96.71 12.69 1.50e+00 4.44e-01 7.16e+01 angle pdb=" C3' C G 8 " pdb=" O3' C G 8 " pdb=" P A G 9 " ideal model delta sigma weight residual 120.20 130.50 -10.30 1.50e+00 4.44e-01 4.71e+01 angle pdb=" CA ASP E 122 " pdb=" CB ASP E 122 " pdb=" CG ASP E 122 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.00e+00 1.00e+00 3.12e+01 angle pdb=" C4' A G 19 " pdb=" C3' A G 19 " pdb=" O3' A G 19 " ideal model delta sigma weight residual 113.00 121.30 -8.30 1.50e+00 4.44e-01 3.06e+01 angle pdb=" C4' U G 26 " pdb=" C3' U G 26 " pdb=" O3' U G 26 " ideal model delta sigma weight residual 109.40 117.20 -7.80 1.50e+00 4.44e-01 2.71e+01 ... (remaining 24074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 10487 35.89 - 71.79: 195 71.79 - 107.68: 20 107.68 - 143.58: 2 143.58 - 179.47: 2 Dihedral angle restraints: 10706 sinusoidal: 4667 harmonic: 6039 Sorted by residual: dihedral pdb=" O4' C G 10 " pdb=" C1' C G 10 " pdb=" N1 C G 10 " pdb=" C2 C G 10 " ideal model delta sinusoidal sigma weight residual -160.00 -2.54 -157.46 1 1.50e+01 4.44e-03 8.21e+01 dihedral pdb=" CB CYS F 410 " pdb=" SG CYS F 410 " pdb=" SG CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sinusoidal sigma weight residual -86.00 -158.19 72.19 1 1.00e+01 1.00e-02 6.66e+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 232.00 52.53 179.47 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 10703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2093 0.066 - 0.132: 466 0.132 - 0.198: 67 0.198 - 0.264: 19 0.264 - 0.330: 6 Chirality restraints: 2651 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" P G G 5 " pdb=" OP1 G G 5 " pdb=" OP2 G G 5 " pdb=" O5' G G 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE C 91 " pdb=" CA ILE C 91 " pdb=" CG1 ILE C 91 " pdb=" CG2 ILE C 91 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2648 not shown) Planarity restraints: 2973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 339 " -0.031 2.00e-02 2.50e+03 3.09e-02 2.39e+01 pdb=" CG TRP F 339 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP F 339 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP F 339 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 339 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP F 339 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 339 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 339 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 339 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP F 339 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 85 " -0.022 2.00e-02 2.50e+03 2.21e-02 8.51e+00 pdb=" CG PHE I 85 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE I 85 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE I 85 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE I 85 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE I 85 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE I 85 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 72 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" CG ASP F 72 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP F 72 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP F 72 " -0.014 2.00e-02 2.50e+03 ... (remaining 2970 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 152 2.62 - 3.19: 15977 3.19 - 3.76: 25525 3.76 - 4.33: 36218 4.33 - 4.90: 58169 Nonbonded interactions: 136041 Sorted by model distance: nonbonded pdb=" O ARG A 144 " pdb=" OE1 GLN C 40 " model vdw 2.048 3.040 nonbonded pdb=" O LEU E 55 " pdb=" OG1 THR E 58 " model vdw 2.098 3.040 nonbonded pdb=" NH2 ARG A 129 " pdb=" OD1 ASN C 57 " model vdw 2.158 3.120 nonbonded pdb=" O PHE F 344 " pdb=" OG1 THR F 345 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR F 499 " pdb=" O GLU F 574 " model vdw 2.265 3.040 ... (remaining 136036 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: 0.730 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: 0.050 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.170 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 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 0.052 17802 Z= 0.349 Angle : 0.931 12.691 24081 Z= 0.551 Chirality : 0.058 0.330 2651 Planarity : 0.004 0.041 2973 Dihedral : 14.119 179.472 6817 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.85 % Favored : 95.10 % Rotamer: Outliers : 0.65 % Allowed : 0.76 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.17), residues: 2022 helix: 0.01 (0.17), residues: 878 sheet: -0.02 (0.28), residues: 336 loop : -1.86 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 137 TYR 0.024 0.002 TYR E 189 PHE 0.051 0.003 PHE I 85 TRP 0.079 0.004 TRP F 339 HIS 0.007 0.002 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00609 (17801) covalent geometry : angle 0.93108 (24079) SS BOND : bond 0.00184 ( 1) SS BOND : angle 1.33581 ( 2) hydrogen bonds : bond 0.18100 ( 800) hydrogen bonds : angle 7.19168 ( 2325) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 287 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.8202 (tp) cc_final: 0.7857 (mp) REVERT: B 17 LEU cc_start: 0.9298 (tt) cc_final: 0.8437 (mt) REVERT: B 46 ILE cc_start: 0.8693 (tt) cc_final: 0.8450 (pt) REVERT: B 115 ASP cc_start: 0.8646 (t0) cc_final: 0.8183 (m-30) REVERT: E 66 PRO cc_start: 0.8088 (Cg_exo) cc_final: 0.7560 (Cg_endo) REVERT: F 13 LEU cc_start: 0.9263 (mt) cc_final: 0.8989 (mp) REVERT: F 588 LEU cc_start: 0.8993 (tp) cc_final: 0.8437 (mm) REVERT: F 669 LYS cc_start: 0.9187 (mttt) cc_final: 0.8687 (pttp) REVERT: H 10 LEU cc_start: 0.8266 (mp) cc_final: 0.7779 (mt) REVERT: I 18 HIS cc_start: 0.8633 (t70) cc_final: 0.8236 (t-170) REVERT: I 74 PHE cc_start: 0.9166 (t80) cc_final: 0.8894 (t80) REVERT: I 75 ILE cc_start: 0.9155 (mm) cc_final: 0.8635 (mm) REVERT: I 102 THR cc_start: 0.9069 (p) cc_final: 0.8726 (p) REVERT: I 107 ILE cc_start: 0.8904 (mt) cc_final: 0.8421 (tp) REVERT: K 127 PHE cc_start: 0.8674 (t80) cc_final: 0.8474 (t80) outliers start: 12 outliers final: 5 residues processed: 296 average time/residue: 0.1610 time to fit residues: 67.6681 Evaluate side-chains 163 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 174 HIS ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN E 255 GLN E 316 ASN E 324 GLN ** F 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 HIS F 26 HIS F 33 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN F 472 ASN F 482 ASN F 560 GLN F 681 GLN F 708 ASN H 17 HIS ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.049437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.042150 restraints weight = 251425.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.043058 restraints weight = 157998.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.043648 restraints weight = 109578.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.044060 restraints weight = 83848.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.044320 restraints weight = 69737.097| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17802 Z= 0.196 Angle : 0.683 11.350 24081 Z= 0.369 Chirality : 0.044 0.241 2651 Planarity : 0.004 0.042 2973 Dihedral : 13.681 173.570 2654 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.16 % Allowed : 2.81 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.18), residues: 2022 helix: 0.67 (0.17), residues: 914 sheet: -0.04 (0.27), residues: 373 loop : -1.74 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 190 TYR 0.023 0.002 TYR E 95 PHE 0.032 0.002 PHE I 85 TRP 0.036 0.002 TRP F 339 HIS 0.021 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00384 (17801) covalent geometry : angle 0.68331 (24079) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.61322 ( 2) hydrogen bonds : bond 0.04693 ( 800) hydrogen bonds : angle 5.41691 ( 2325) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LEU cc_start: 0.9847 (tt) cc_final: 0.9144 (mt) REVERT: B 46 ILE cc_start: 0.9795 (tt) cc_final: 0.9528 (pt) REVERT: B 55 MET cc_start: 0.9530 (mmp) cc_final: 0.9329 (mmm) REVERT: B 115 ASP cc_start: 0.9651 (t0) cc_final: 0.8988 (m-30) REVERT: C 55 MET cc_start: 0.9453 (tpt) cc_final: 0.9218 (tpt) REVERT: E 24 MET cc_start: 0.6840 (ttt) cc_final: 0.6324 (tpp) REVERT: E 49 PHE cc_start: 0.9637 (t80) cc_final: 0.9380 (t80) REVERT: F 163 MET cc_start: 0.9427 (ptp) cc_final: 0.9218 (ptt) REVERT: F 496 MET cc_start: 0.6981 (ppp) cc_final: 0.6450 (pmm) REVERT: F 588 LEU cc_start: 0.9949 (tp) cc_final: 0.9684 (mm) REVERT: F 589 PHE cc_start: 0.9691 (t80) cc_final: 0.9296 (t80) REVERT: I 85 PHE cc_start: 0.9669 (m-80) cc_final: 0.9465 (m-80) REVERT: I 86 TYR cc_start: 0.9062 (m-80) cc_final: 0.8848 (m-80) REVERT: I 107 ILE cc_start: 0.8810 (mt) cc_final: 0.8507 (tp) REVERT: I 120 PHE cc_start: 0.9717 (t80) cc_final: 0.9339 (t80) REVERT: I 137 TYR cc_start: 0.7479 (m-10) cc_final: 0.7191 (m-80) REVERT: K 123 TYR cc_start: 0.9827 (t80) cc_final: 0.9613 (t80) REVERT: K 126 TYR cc_start: 0.9249 (m-10) cc_final: 0.9041 (m-80) REVERT: K 127 PHE cc_start: 0.9863 (t80) cc_final: 0.9552 (t80) outliers start: 3 outliers final: 0 residues processed: 178 average time/residue: 0.1408 time to fit residues: 37.7821 Evaluate side-chains 127 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 52 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 143 optimal weight: 0.5980 chunk 202 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 HIS ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 HIS E 324 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN F 169 HIS F 242 ASN F 306 ASN F 549 ASN H 207 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.047008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.039838 restraints weight = 261610.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040625 restraints weight = 162517.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.041181 restraints weight = 115527.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.041592 restraints weight = 89439.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.041879 restraints weight = 73729.752| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17802 Z= 0.174 Angle : 0.617 7.740 24081 Z= 0.329 Chirality : 0.042 0.279 2651 Planarity : 0.003 0.034 2973 Dihedral : 13.532 174.791 2654 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.16 % Allowed : 2.92 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.18), residues: 2022 helix: 0.90 (0.17), residues: 914 sheet: 0.15 (0.27), residues: 379 loop : -1.64 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 78 TYR 0.024 0.002 TYR E 57 PHE 0.032 0.002 PHE K 85 TRP 0.026 0.002 TRP F 339 HIS 0.013 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00350 (17801) covalent geometry : angle 0.61723 (24079) SS BOND : bond 0.01596 ( 1) SS BOND : angle 1.49448 ( 2) hydrogen bonds : bond 0.04087 ( 800) hydrogen bonds : angle 5.13262 ( 2325) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9679 (mmt) cc_final: 0.9475 (mmp) REVERT: B 46 ILE cc_start: 0.9820 (tt) cc_final: 0.9557 (pt) REVERT: B 115 ASP cc_start: 0.9718 (t0) cc_final: 0.9059 (m-30) REVERT: C 55 MET cc_start: 0.9446 (tpt) cc_final: 0.9206 (tpt) REVERT: E 24 MET cc_start: 0.7043 (ttt) cc_final: 0.6215 (tpp) REVERT: E 49 PHE cc_start: 0.9437 (t80) cc_final: 0.9209 (t80) REVERT: E 51 LYS cc_start: 0.9454 (mmpt) cc_final: 0.9232 (mmmt) REVERT: E 119 MET cc_start: 0.8228 (mmt) cc_final: 0.7851 (mmt) REVERT: F 47 PHE cc_start: 0.7847 (m-80) cc_final: 0.7299 (m-80) REVERT: F 189 TRP cc_start: 0.9256 (m-10) cc_final: 0.9003 (m-10) REVERT: F 363 MET cc_start: 0.7279 (mmm) cc_final: 0.7025 (mmm) REVERT: F 420 ASP cc_start: 0.9654 (m-30) cc_final: 0.9127 (t0) REVERT: F 589 PHE cc_start: 0.9737 (t80) cc_final: 0.9396 (t80) REVERT: H 226 MET cc_start: 0.8721 (mmm) cc_final: 0.8404 (mmm) REVERT: I 86 TYR cc_start: 0.8848 (m-80) cc_final: 0.8598 (m-80) REVERT: I 120 PHE cc_start: 0.9670 (t80) cc_final: 0.9383 (t80) REVERT: K 86 TYR cc_start: 0.9642 (m-10) cc_final: 0.9371 (m-10) REVERT: K 123 TYR cc_start: 0.9869 (t80) cc_final: 0.9592 (t80) REVERT: K 126 TYR cc_start: 0.9297 (m-10) cc_final: 0.9078 (m-80) REVERT: K 127 PHE cc_start: 0.9821 (t80) cc_final: 0.9247 (t80) outliers start: 3 outliers final: 1 residues processed: 156 average time/residue: 0.1364 time to fit residues: 32.4188 Evaluate side-chains 115 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 41 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 99 optimal weight: 0.8980 chunk 192 optimal weight: 0.0770 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 174 HIS ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 168 ASN E 324 GLN ** F 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 HIS H 129 GLN H 177 ASN ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 HIS I 27 ASN K 41 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.044304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.037247 restraints weight = 269056.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038027 restraints weight = 167359.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.038568 restraints weight = 116858.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.038943 restraints weight = 91402.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039179 restraints weight = 75907.741| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17802 Z= 0.186 Angle : 0.615 8.495 24081 Z= 0.332 Chirality : 0.042 0.255 2651 Planarity : 0.003 0.035 2973 Dihedral : 13.438 175.396 2654 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.18), residues: 2022 helix: 0.85 (0.17), residues: 909 sheet: 0.21 (0.28), residues: 351 loop : -1.53 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 405 TYR 0.026 0.002 TYR H 184 PHE 0.070 0.002 PHE I 85 TRP 0.023 0.002 TRP F 339 HIS 0.008 0.002 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00370 (17801) covalent geometry : angle 0.61456 (24079) SS BOND : bond 0.00504 ( 1) SS BOND : angle 2.94799 ( 2) hydrogen bonds : bond 0.03941 ( 800) hydrogen bonds : angle 5.10967 ( 2325) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.9584 (mmp) cc_final: 0.9380 (mmm) REVERT: B 115 ASP cc_start: 0.9471 (t0) cc_final: 0.9266 (m-30) REVERT: E 24 MET cc_start: 0.7621 (ttt) cc_final: 0.6282 (ppp) REVERT: E 49 PHE cc_start: 0.9299 (t80) cc_final: 0.9020 (t80) REVERT: E 62 PHE cc_start: 0.9172 (m-10) cc_final: 0.8958 (m-80) REVERT: E 119 MET cc_start: 0.8922 (mmt) cc_final: 0.8663 (mmt) REVERT: E 129 LEU cc_start: 0.9872 (mt) cc_final: 0.9670 (tp) REVERT: F 363 MET cc_start: 0.7325 (mmm) cc_final: 0.7122 (mmm) REVERT: F 420 ASP cc_start: 0.9610 (m-30) cc_final: 0.8883 (t0) REVERT: F 589 PHE cc_start: 0.9646 (t80) cc_final: 0.9358 (t80) REVERT: H 28 MET cc_start: 0.9674 (mtp) cc_final: 0.9378 (ttt) REVERT: H 187 LEU cc_start: 0.9773 (mt) cc_final: 0.9542 (pp) REVERT: I 86 TYR cc_start: 0.8890 (m-80) cc_final: 0.8665 (m-80) REVERT: I 120 PHE cc_start: 0.9601 (t80) cc_final: 0.9308 (t80) REVERT: K 86 TYR cc_start: 0.9678 (m-10) cc_final: 0.9397 (m-10) REVERT: K 123 TYR cc_start: 0.9872 (t80) cc_final: 0.9477 (t80) REVERT: K 126 TYR cc_start: 0.9220 (m-10) cc_final: 0.8983 (m-80) REVERT: K 127 PHE cc_start: 0.9827 (t80) cc_final: 0.9340 (t80) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.1433 time to fit residues: 30.7923 Evaluate side-chains 104 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 121 optimal weight: 2.9990 chunk 21 optimal weight: 0.0050 chunk 95 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 324 GLN F 73 ASN ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.044897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.037827 restraints weight = 265135.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.038604 restraints weight = 165239.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.039172 restraints weight = 115968.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.039476 restraints weight = 88126.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.039755 restraints weight = 74768.141| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17802 Z= 0.123 Angle : 0.545 7.622 24081 Z= 0.291 Chirality : 0.041 0.214 2651 Planarity : 0.003 0.039 2973 Dihedral : 13.309 174.142 2654 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.16 % Allowed : 1.24 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 2022 helix: 1.08 (0.17), residues: 914 sheet: 0.20 (0.28), residues: 364 loop : -1.51 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 530 TYR 0.021 0.001 TYR E 57 PHE 0.029 0.001 PHE K 85 TRP 0.017 0.001 TRP F 339 HIS 0.005 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00253 (17801) covalent geometry : angle 0.54531 (24079) SS BOND : bond 0.00277 ( 1) SS BOND : angle 1.60128 ( 2) hydrogen bonds : bond 0.03566 ( 800) hydrogen bonds : angle 4.89435 ( 2325) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9645 (mmt) cc_final: 0.9375 (mmp) REVERT: E 24 MET cc_start: 0.7452 (ttt) cc_final: 0.6153 (ppp) REVERT: E 51 LYS cc_start: 0.9286 (mmpt) cc_final: 0.8980 (mmmt) REVERT: E 62 PHE cc_start: 0.9211 (m-10) cc_final: 0.8983 (m-80) REVERT: F 1 MET cc_start: 0.7785 (tpt) cc_final: 0.7448 (tmm) REVERT: F 420 ASP cc_start: 0.9616 (m-30) cc_final: 0.8897 (t0) REVERT: F 496 MET cc_start: 0.7694 (ppp) cc_final: 0.7398 (pmm) REVERT: F 589 PHE cc_start: 0.9630 (t80) cc_final: 0.9331 (t80) REVERT: H 28 MET cc_start: 0.9711 (mtp) cc_final: 0.9444 (ttt) REVERT: H 129 GLN cc_start: 0.9592 (mm110) cc_final: 0.9278 (mp10) REVERT: H 187 LEU cc_start: 0.9799 (mt) cc_final: 0.9556 (pp) REVERT: H 226 MET cc_start: 0.9435 (tpt) cc_final: 0.8748 (mmm) REVERT: I 86 TYR cc_start: 0.8877 (m-80) cc_final: 0.8652 (m-80) REVERT: I 120 PHE cc_start: 0.9505 (t80) cc_final: 0.9275 (t80) REVERT: K 86 TYR cc_start: 0.9665 (m-10) cc_final: 0.9354 (m-80) REVERT: K 123 TYR cc_start: 0.9861 (t80) cc_final: 0.9451 (t80) REVERT: K 126 TYR cc_start: 0.9210 (m-10) cc_final: 0.8962 (m-80) REVERT: K 127 PHE cc_start: 0.9819 (t80) cc_final: 0.9273 (t80) outliers start: 3 outliers final: 1 residues processed: 136 average time/residue: 0.1391 time to fit residues: 28.9244 Evaluate side-chains 108 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN E 324 GLN ** F 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.041798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.034970 restraints weight = 278946.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.035714 restraints weight = 173455.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.036150 restraints weight = 121886.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.036523 restraints weight = 95438.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036766 restraints weight = 80022.315| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17802 Z= 0.219 Angle : 0.646 11.386 24081 Z= 0.348 Chirality : 0.042 0.223 2651 Planarity : 0.004 0.038 2973 Dihedral : 13.395 175.621 2654 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.18), residues: 2022 helix: 0.75 (0.17), residues: 910 sheet: -0.04 (0.28), residues: 351 loop : -1.42 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 477 TYR 0.021 0.002 TYR E 57 PHE 0.068 0.002 PHE I 85 TRP 0.026 0.002 TRP H 52 HIS 0.007 0.002 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00436 (17801) covalent geometry : angle 0.64554 (24079) SS BOND : bond 0.00853 ( 1) SS BOND : angle 1.67592 ( 2) hydrogen bonds : bond 0.03971 ( 800) hydrogen bonds : angle 5.16665 ( 2325) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9445 (mmt) cc_final: 0.9149 (mmp) REVERT: E 24 MET cc_start: 0.7764 (ttt) cc_final: 0.7158 (ppp) REVERT: E 49 PHE cc_start: 0.9571 (t80) cc_final: 0.9167 (t80) REVERT: E 51 LYS cc_start: 0.9440 (mmpt) cc_final: 0.9112 (mmmt) REVERT: E 62 PHE cc_start: 0.9343 (m-10) cc_final: 0.9091 (m-80) REVERT: E 119 MET cc_start: 0.8538 (mmt) cc_final: 0.8335 (mmt) REVERT: F 189 TRP cc_start: 0.9551 (m-10) cc_final: 0.8965 (m-10) REVERT: F 363 MET cc_start: 0.8141 (tpt) cc_final: 0.7843 (mmm) REVERT: F 420 ASP cc_start: 0.9608 (m-30) cc_final: 0.9285 (t0) REVERT: F 589 PHE cc_start: 0.9570 (t80) cc_final: 0.9260 (t80) REVERT: H 28 MET cc_start: 0.9592 (mtp) cc_final: 0.9320 (ttt) REVERT: H 187 LEU cc_start: 0.9755 (mt) cc_final: 0.9481 (pp) REVERT: I 14 MET cc_start: 0.9521 (tmm) cc_final: 0.9307 (tmm) REVERT: I 86 TYR cc_start: 0.8921 (m-80) cc_final: 0.8260 (m-80) REVERT: I 105 PHE cc_start: 0.9027 (m-80) cc_final: 0.8819 (m-10) REVERT: I 120 PHE cc_start: 0.9531 (t80) cc_final: 0.9297 (t80) REVERT: K 86 TYR cc_start: 0.9681 (m-10) cc_final: 0.9363 (m-80) REVERT: K 109 ASP cc_start: 0.9611 (t70) cc_final: 0.9244 (m-30) REVERT: K 123 TYR cc_start: 0.9841 (t80) cc_final: 0.9388 (t80) REVERT: K 126 TYR cc_start: 0.9186 (m-10) cc_final: 0.8918 (m-80) REVERT: K 127 PHE cc_start: 0.9792 (t80) cc_final: 0.9213 (t80) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.1373 time to fit residues: 26.4810 Evaluate side-chains 99 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 78 optimal weight: 0.3980 chunk 177 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 108 optimal weight: 0.0570 chunk 42 optimal weight: 9.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 324 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 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 = 0.3117 r_free = 0.3117 target = 0.044244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.037374 restraints weight = 266952.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.038182 restraints weight = 161539.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.038664 restraints weight = 110265.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.039034 restraints weight = 86504.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.039282 restraints weight = 71524.434| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17802 Z= 0.104 Angle : 0.545 9.617 24081 Z= 0.286 Chirality : 0.041 0.311 2651 Planarity : 0.003 0.043 2973 Dihedral : 13.244 174.336 2654 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.05 % Allowed : 1.24 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 2022 helix: 1.13 (0.17), residues: 910 sheet: 0.02 (0.28), residues: 363 loop : -1.37 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 91 TYR 0.017 0.001 TYR I 80 PHE 0.024 0.001 PHE K 85 TRP 0.012 0.001 TRP F 339 HIS 0.005 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00211 (17801) covalent geometry : angle 0.54468 (24079) SS BOND : bond 0.00181 ( 1) SS BOND : angle 0.98120 ( 2) hydrogen bonds : bond 0.03385 ( 800) hydrogen bonds : angle 4.85381 ( 2325) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.634 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 55 MET cc_start: 0.9638 (mmt) cc_final: 0.9370 (mmp) REVERT: E 24 MET cc_start: 0.7677 (ttt) cc_final: 0.7057 (ppp) REVERT: E 62 PHE cc_start: 0.9274 (m-10) cc_final: 0.9021 (m-80) REVERT: F 363 MET cc_start: 0.8024 (tpt) cc_final: 0.7740 (mmm) REVERT: F 420 ASP cc_start: 0.9740 (m-30) cc_final: 0.8984 (t0) REVERT: F 496 MET cc_start: 0.6542 (pmm) cc_final: 0.5994 (pmm) REVERT: F 589 PHE cc_start: 0.9608 (t80) cc_final: 0.9317 (t80) REVERT: H 28 MET cc_start: 0.9693 (mtp) cc_final: 0.9370 (ttt) REVERT: H 129 GLN cc_start: 0.9705 (mm110) cc_final: 0.9337 (mp10) REVERT: H 187 LEU cc_start: 0.9766 (mt) cc_final: 0.9536 (pp) REVERT: I 14 MET cc_start: 0.9415 (tmm) cc_final: 0.9197 (tmm) REVERT: I 86 TYR cc_start: 0.8785 (m-80) cc_final: 0.8228 (m-80) REVERT: K 54 GLN cc_start: 0.9755 (tp-100) cc_final: 0.9266 (tm-30) REVERT: K 86 TYR cc_start: 0.9664 (m-10) cc_final: 0.9350 (m-80) REVERT: K 123 TYR cc_start: 0.9817 (t80) cc_final: 0.9500 (t80) REVERT: K 126 TYR cc_start: 0.9197 (m-10) cc_final: 0.8967 (m-80) REVERT: K 127 PHE cc_start: 0.9804 (t80) cc_final: 0.9267 (t80) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.1336 time to fit residues: 25.8219 Evaluate side-chains 105 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 195 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 ASN ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.039681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032968 restraints weight = 291434.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.033596 restraints weight = 184703.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.034066 restraints weight = 132995.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.034352 restraints weight = 102705.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.034487 restraints weight = 87082.853| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.6975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17802 Z= 0.292 Angle : 0.746 8.699 24081 Z= 0.403 Chirality : 0.045 0.317 2651 Planarity : 0.004 0.054 2973 Dihedral : 13.532 176.996 2654 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.18), residues: 2022 helix: 0.30 (0.16), residues: 922 sheet: -0.50 (0.27), residues: 355 loop : -1.44 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 110 TYR 0.027 0.002 TYR E 57 PHE 0.022 0.003 PHE H 283 TRP 0.024 0.002 TRP H 52 HIS 0.011 0.002 HIS F 169 Details of bonding type rmsd covalent geometry : bond 0.00572 (17801) covalent geometry : angle 0.74608 (24079) SS BOND : bond 0.01117 ( 1) SS BOND : angle 1.57651 ( 2) hydrogen bonds : bond 0.04494 ( 800) hydrogen bonds : angle 5.45586 ( 2325) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.674 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: A 55 MET cc_start: 0.9536 (mmt) cc_final: 0.9295 (mmp) REVERT: E 49 PHE cc_start: 0.9512 (t80) cc_final: 0.9098 (t80) REVERT: E 62 PHE cc_start: 0.9338 (m-10) cc_final: 0.9116 (m-80) REVERT: F 1 MET cc_start: 0.8026 (tmm) cc_final: 0.7745 (tmm) REVERT: F 363 MET cc_start: 0.8269 (tpt) cc_final: 0.8062 (mmm) REVERT: F 420 ASP cc_start: 0.9796 (m-30) cc_final: 0.9314 (t0) REVERT: F 589 PHE cc_start: 0.9623 (t80) cc_final: 0.9378 (t80) REVERT: H 28 MET cc_start: 0.9634 (mtp) cc_final: 0.9251 (ttt) REVERT: I 69 GLN cc_start: 0.9133 (tp40) cc_final: 0.8921 (tp40) REVERT: I 86 TYR cc_start: 0.8875 (m-80) cc_final: 0.8332 (m-80) REVERT: I 120 PHE cc_start: 0.9415 (t80) cc_final: 0.9193 (t80) REVERT: K 109 ASP cc_start: 0.9721 (t0) cc_final: 0.9463 (m-30) REVERT: K 123 TYR cc_start: 0.9843 (t80) cc_final: 0.9478 (t80) REVERT: K 126 TYR cc_start: 0.9218 (m-10) cc_final: 0.9002 (m-80) REVERT: K 127 PHE cc_start: 0.9818 (t80) cc_final: 0.9286 (t80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1367 time to fit residues: 24.5649 Evaluate side-chains 91 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 113 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 162 optimal weight: 0.0980 chunk 178 optimal weight: 9.9990 chunk 82 optimal weight: 0.2980 chunk 76 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS E 220 GLN E 324 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.041920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.035089 restraints weight = 277293.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.035799 restraints weight = 170286.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.036329 restraints weight = 120620.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.036648 restraints weight = 91792.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.036890 restraints weight = 76252.123| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.6813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17802 Z= 0.124 Angle : 0.574 8.926 24081 Z= 0.304 Chirality : 0.041 0.269 2651 Planarity : 0.003 0.062 2973 Dihedral : 13.386 174.764 2654 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.11 % Allowed : 0.43 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.18), residues: 2022 helix: 0.84 (0.17), residues: 918 sheet: -0.41 (0.28), residues: 360 loop : -1.30 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 110 TYR 0.022 0.002 TYR I 86 PHE 0.023 0.002 PHE K 85 TRP 0.014 0.002 TRP E 89 HIS 0.005 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00252 (17801) covalent geometry : angle 0.57364 (24079) SS BOND : bond 0.00389 ( 1) SS BOND : angle 1.27740 ( 2) hydrogen bonds : bond 0.03535 ( 800) hydrogen bonds : angle 5.07572 ( 2325) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9609 (mmt) cc_final: 0.9319 (mmp) REVERT: E 24 MET cc_start: 0.8503 (tpt) cc_final: 0.7905 (ppp) REVERT: E 40 MET cc_start: 0.9309 (mmp) cc_final: 0.8799 (tmm) REVERT: E 62 PHE cc_start: 0.9257 (m-10) cc_final: 0.9028 (m-80) REVERT: F 1 MET cc_start: 0.7838 (tmm) cc_final: 0.7635 (tmm) REVERT: F 420 ASP cc_start: 0.9796 (m-30) cc_final: 0.9337 (t0) REVERT: F 452 MET cc_start: 0.9006 (mmp) cc_final: 0.8784 (mmm) REVERT: F 496 MET cc_start: 0.5306 (pmm) cc_final: 0.4798 (pmm) REVERT: F 589 PHE cc_start: 0.9628 (t80) cc_final: 0.9404 (t80) REVERT: H 28 MET cc_start: 0.9659 (mtp) cc_final: 0.9311 (ttt) REVERT: H 226 MET cc_start: 0.8856 (tpp) cc_final: 0.7799 (mmm) REVERT: I 14 MET cc_start: 0.9440 (tmm) cc_final: 0.9231 (tmm) REVERT: I 49 ARG cc_start: 0.9035 (mtm180) cc_final: 0.8641 (ptt180) REVERT: I 69 GLN cc_start: 0.9148 (tp40) cc_final: 0.8930 (tp40) REVERT: I 87 TYR cc_start: 0.8666 (t80) cc_final: 0.8429 (t80) REVERT: K 45 THR cc_start: 0.9610 (p) cc_final: 0.9323 (p) REVERT: K 52 MET cc_start: 0.9790 (ptp) cc_final: 0.9241 (tpt) REVERT: K 86 TYR cc_start: 0.9588 (m-10) cc_final: 0.9383 (m-80) REVERT: K 109 ASP cc_start: 0.9713 (t0) cc_final: 0.9462 (m-30) REVERT: K 123 TYR cc_start: 0.9813 (t80) cc_final: 0.9507 (t80) REVERT: K 126 TYR cc_start: 0.9189 (m-10) cc_final: 0.8955 (m-80) REVERT: K 127 PHE cc_start: 0.9786 (t80) cc_final: 0.9128 (t80) outliers start: 2 outliers final: 0 residues processed: 120 average time/residue: 0.1413 time to fit residues: 25.7924 Evaluate side-chains 95 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 190 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 184 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 179 optimal weight: 0.9990 chunk 141 optimal weight: 0.0770 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.042980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.036122 restraints weight = 271373.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.036876 restraints weight = 166041.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.037389 restraints weight = 116078.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.037716 restraints weight = 88619.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.037981 restraints weight = 73379.218| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17802 Z= 0.104 Angle : 0.550 9.308 24081 Z= 0.289 Chirality : 0.041 0.262 2651 Planarity : 0.003 0.072 2973 Dihedral : 13.166 173.659 2654 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.18), residues: 2022 helix: 1.04 (0.17), residues: 925 sheet: -0.24 (0.28), residues: 353 loop : -1.27 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 110 TYR 0.021 0.001 TYR E 57 PHE 0.014 0.001 PHE E 92 TRP 0.029 0.002 TRP H 52 HIS 0.008 0.001 HIS H 174 Details of bonding type rmsd covalent geometry : bond 0.00212 (17801) covalent geometry : angle 0.55030 (24079) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.64350 ( 2) hydrogen bonds : bond 0.03345 ( 800) hydrogen bonds : angle 4.84550 ( 2325) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.572 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: A 55 MET cc_start: 0.9605 (mmt) cc_final: 0.9277 (mmp) REVERT: E 24 MET cc_start: 0.8836 (tpt) cc_final: 0.8223 (ppp) REVERT: E 40 MET cc_start: 0.9302 (mmp) cc_final: 0.8785 (tmm) REVERT: E 62 PHE cc_start: 0.9309 (m-10) cc_final: 0.9085 (m-80) REVERT: F 1 MET cc_start: 0.7707 (tmm) cc_final: 0.7502 (tmm) REVERT: F 47 PHE cc_start: 0.8208 (m-80) cc_final: 0.7400 (m-80) REVERT: F 189 TRP cc_start: 0.9408 (m-10) cc_final: 0.9018 (m-10) REVERT: F 420 ASP cc_start: 0.9803 (m-30) cc_final: 0.9358 (t0) REVERT: F 452 MET cc_start: 0.8981 (mmp) cc_final: 0.8753 (mmm) REVERT: F 496 MET cc_start: 0.5077 (pmm) cc_final: 0.4618 (pmm) REVERT: F 624 MET cc_start: 0.8255 (mmm) cc_final: 0.7896 (mpp) REVERT: H 28 MET cc_start: 0.9649 (mtp) cc_final: 0.9326 (ttt) REVERT: H 129 GLN cc_start: 0.9718 (mm110) cc_final: 0.9446 (mp10) REVERT: H 226 MET cc_start: 0.8777 (tpp) cc_final: 0.7735 (mmm) REVERT: I 69 GLN cc_start: 0.9211 (tp40) cc_final: 0.8970 (tp40) REVERT: I 86 TYR cc_start: 0.8838 (m-80) cc_final: 0.8545 (m-80) REVERT: I 120 PHE cc_start: 0.9508 (t80) cc_final: 0.9243 (t80) REVERT: K 14 MET cc_start: 0.5746 (mmt) cc_final: 0.5530 (mmt) REVERT: K 86 TYR cc_start: 0.9662 (m-10) cc_final: 0.9370 (m-80) REVERT: K 109 ASP cc_start: 0.9768 (t0) cc_final: 0.9550 (m-30) REVERT: K 123 TYR cc_start: 0.9847 (t80) cc_final: 0.9413 (t80) REVERT: K 126 TYR cc_start: 0.9192 (m-10) cc_final: 0.8948 (m-80) REVERT: K 127 PHE cc_start: 0.9799 (t80) cc_final: 0.9255 (t80) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1280 time to fit residues: 24.5484 Evaluate side-chains 98 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 4 optimal weight: 7.9990 chunk 188 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 71 optimal weight: 0.0370 chunk 20 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.039772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.032969 restraints weight = 291791.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.033645 restraints weight = 182168.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.034114 restraints weight = 129739.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.034417 restraints weight = 100107.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.034637 restraints weight = 84116.596| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.7439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17802 Z= 0.248 Angle : 0.675 8.933 24081 Z= 0.363 Chirality : 0.043 0.284 2651 Planarity : 0.004 0.068 2973 Dihedral : 13.346 176.654 2654 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.18), residues: 2022 helix: 0.67 (0.17), residues: 921 sheet: -0.64 (0.27), residues: 357 loop : -1.33 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 22 TYR 0.027 0.002 TYR I 86 PHE 0.018 0.002 PHE I 105 TRP 0.020 0.002 TRP F 184 HIS 0.008 0.002 HIS F 169 Details of bonding type rmsd covalent geometry : bond 0.00485 (17801) covalent geometry : angle 0.67490 (24079) SS BOND : bond 0.00919 ( 1) SS BOND : angle 1.20124 ( 2) hydrogen bonds : bond 0.04126 ( 800) hydrogen bonds : angle 5.24310 ( 2325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2262.28 seconds wall clock time: 40 minutes 28.73 seconds (2428.73 seconds total)