Starting phenix.real_space_refine on Sat Sep 12 19:02:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v02_26927/09_2026/7v02_26927_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v02_26927/09_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_26927/09_2026/7v02_26927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v02_26927/09_2026/7v02_26927.map" model { file = "/net/cci-nas-00/data/ceres_data/7v02_26927/09_2026/7v02_26927_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v02_26927/09_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-2.2.1-6174/lib/python3.11/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: 4.17, per 1000 atoms: 0.24 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: 1.72 Conformation dependent library (CDL) restraints added in 834.8 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: 2.03 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: 3.20 Time building geometry restraints manager: 2.31 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 1.20e-02 6.94e+03 1.83e+01 bond pdb=" O3' A G 7 " pdb=" P C G 8 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.20e-02 6.94e+03 1.42e+01 bond pdb=" O3' G G 5 " pdb=" P A G 6 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.20e-02 6.94e+03 1.39e+01 bond pdb=" O3' U G 24 " pdb=" P A G 25 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.20e-02 6.94e+03 1.36e+01 bond pdb=" C3' U G 24 " pdb=" O3' U G 24 " ideal model delta sigma weight residual 1.417 1.466 -0.049 1.40e-02 5.10e+03 1.22e+01 ... (remaining 17796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 23407 2.54 - 5.08: 579 5.08 - 7.61: 79 7.61 - 10.15: 10 10.15 - 12.69: 4 Bond angle restraints: 24079 Sorted by residual: angle pdb=" C3' C G 8 " pdb=" O3' C G 8 " pdb=" P A G 9 " ideal model delta sigma weight residual 119.70 130.50 -10.80 1.20e+00 6.94e-01 8.10e+01 angle pdb=" C3' U G 24 " pdb=" O3' U G 24 " pdb=" P A G 25 " ideal model delta sigma weight residual 119.70 127.04 -7.34 1.20e+00 6.94e-01 3.74e+01 angle pdb=" O4' G G 3 " pdb=" C4' G G 3 " pdb=" C3' G G 3 " ideal model delta sigma weight residual 106.10 101.23 4.87 8.00e-01 1.56e+00 3.70e+01 angle pdb=" C3' G G 3 " pdb=" C2' G G 3 " pdb=" C1' G G 3 " ideal model delta sigma weight residual 101.50 96.66 4.84 8.00e-01 1.56e+00 3.65e+01 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 2.10e+00 2.27e-01 3.65e+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: 2086 0.066 - 0.132: 480 0.132 - 0.198: 64 0.198 - 0.264: 15 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.220 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 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= 0.367 Angle : 0.932 12.691 24081 Z= 0.568 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/Z covalent geometry : bond 0.00610 / 0.37 (17801) covalent geometry : angle 0.93146 / 0.57 (24079) SS BOND : bond 0.00184 / 0.10 ( 1) SS BOND : angle 1.33581 / 0.70 ( 2) hydrogen bonds : bond 0.18100 / 12.84 ( 800) hydrogen bonds : angle 7.19168 / 4.92 ( 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 : 0.636 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: 0.1716 time to fit residues: 72.4362 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 : 0.683 ------------------------------------------------------------------------------- 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... A 168 ASN B 174 HIS ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** 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 472 ASN F 482 ASN F 560 GLN F 708 ASN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.050753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.043359 restraints weight = 247911.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.044225 restraints weight = 154256.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.044769 restraints weight = 109032.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.045167 restraints weight = 84945.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.045499 restraints weight = 70934.128| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17802 Z= 0.196 Angle : 0.712 10.692 24081 Z= 0.387 Chirality : 0.046 0.224 2651 Planarity : 0.004 0.046 2973 Dihedral : 13.789 176.275 2654 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.16 % Allowed : 2.70 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 2022 helix: 0.53 (0.17), residues: 919 sheet: 0.00 (0.27), residues: 368 loop : -1.84 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 530 TYR 0.027 0.002 TYR H 104 PHE 0.031 0.002 PHE I 85 TRP 0.039 0.002 TRP F 339 HIS 0.017 0.002 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 (17801) covalent geometry : angle 0.71224 / 0.39 (24079) SS BOND : bond 0.00280 / 0.15 ( 1) SS BOND : angle 0.80495 / 0.45 ( 2) hydrogen bonds : bond 0.05110 / 3.56 ( 800) hydrogen bonds : angle 5.62895 / 3.86 ( 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 179 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 0.697 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: B 17 LEU cc_start: 0.9842 (tt) cc_final: 0.9185 (mt) REVERT: B 55 MET cc_start: 0.9536 (mmp) cc_final: 0.9333 (mmm) REVERT: B 115 ASP cc_start: 0.9641 (t0) cc_final: 0.8978 (m-30) REVERT: C 55 MET cc_start: 0.9542 (tpt) cc_final: 0.9224 (tpt) REVERT: E 49 PHE cc_start: 0.9480 (t80) cc_final: 0.9213 (t80) REVERT: F 163 MET cc_start: 0.9451 (ptp) cc_final: 0.9200 (ptp) REVERT: F 363 MET cc_start: 0.7426 (mmm) cc_final: 0.7182 (tpt) REVERT: F 496 MET cc_start: 0.6737 (ppp) cc_final: 0.5683 (pmm) REVERT: F 588 LEU cc_start: 0.9960 (tp) cc_final: 0.9753 (mm) REVERT: F 589 PHE cc_start: 0.9678 (t80) cc_final: 0.9298 (t80) REVERT: F 665 ASP cc_start: 0.9894 (p0) cc_final: 0.9691 (p0) REVERT: H 226 MET cc_start: 0.8898 (mmm) cc_final: 0.8640 (mmm) REVERT: I 85 PHE cc_start: 0.9568 (m-80) cc_final: 0.9366 (m-80) REVERT: I 86 TYR cc_start: 0.8957 (m-80) cc_final: 0.8597 (m-80) REVERT: I 120 PHE cc_start: 0.9537 (t80) cc_final: 0.9243 (t80) REVERT: I 137 TYR cc_start: 0.7506 (m-10) cc_final: 0.7201 (m-80) REVERT: K 27 ASN cc_start: 0.7218 (OUTLIER) cc_final: 0.6743 (m110) REVERT: K 83 ILE cc_start: 0.9640 (mm) cc_final: 0.9312 (mm) REVERT: K 86 TYR cc_start: 0.9722 (m-10) cc_final: 0.9358 (m-80) REVERT: K 126 TYR cc_start: 0.9265 (m-10) cc_final: 0.9053 (m-80) REVERT: K 127 PHE cc_start: 0.9875 (t80) cc_final: 0.9404 (t80) outliers start: 3 outliers final: 0 residues processed: 179 average time/residue: 0.1422 time to fit residues: 38.9313 Evaluate side-chains 128 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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: 0.0970 chunk 1 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 HIS ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 GLN E 316 ASN E 324 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS H 214 GLN I 54 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.049905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.042544 restraints weight = 252427.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.043418 restraints weight = 157394.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.043994 restraints weight = 110701.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.044326 restraints weight = 85880.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.044660 restraints weight = 72489.276| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17802 Z= 0.153 Angle : 0.611 10.762 24081 Z= 0.333 Chirality : 0.043 0.223 2651 Planarity : 0.003 0.042 2973 Dihedral : 13.517 175.342 2654 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.30 % 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: -0.37 (0.18), residues: 2022 helix: 0.76 (0.17), residues: 916 sheet: 0.06 (0.27), residues: 369 loop : -1.67 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 559 TYR 0.021 0.002 TYR F 240 PHE 0.038 0.002 PHE I 40 TRP 0.025 0.002 TRP F 339 HIS 0.013 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (17801) covalent geometry : angle 0.61076 / 0.33 (24079) SS BOND : bond 0.01849 / 0.97 ( 1) SS BOND : angle 3.09731 / 1.69 ( 2) hydrogen bonds : bond 0.04297 / 2.95 ( 800) hydrogen bonds : angle 5.23206 / 3.59 ( 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 157 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.699 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: A 17 LEU cc_start: 0.9928 (tp) cc_final: 0.9334 (mp) REVERT: A 55 MET cc_start: 0.9687 (mmt) cc_final: 0.9484 (mmp) REVERT: B 17 LEU cc_start: 0.9845 (tt) cc_final: 0.9156 (mt) REVERT: B 115 ASP cc_start: 0.9657 (t0) cc_final: 0.8996 (m-30) REVERT: C 55 MET cc_start: 0.9501 (tpt) cc_final: 0.9197 (tpt) REVERT: E 24 MET cc_start: 0.6875 (ttt) cc_final: 0.6067 (tpp) REVERT: E 49 PHE cc_start: 0.9620 (t80) cc_final: 0.9377 (t80) REVERT: F 163 MET cc_start: 0.9336 (ptp) cc_final: 0.9095 (ptp) REVERT: F 318 LEU cc_start: 0.9851 (tp) cc_final: 0.9507 (pp) REVERT: F 496 MET cc_start: 0.6610 (ppp) cc_final: 0.6130 (pmm) REVERT: F 588 LEU cc_start: 0.9922 (tp) cc_final: 0.9693 (mm) REVERT: F 589 PHE cc_start: 0.9664 (t80) cc_final: 0.9245 (t80) REVERT: H 28 MET cc_start: 0.9565 (mtp) cc_final: 0.9362 (ttt) REVERT: I 86 TYR cc_start: 0.9060 (m-80) cc_final: 0.8771 (m-80) REVERT: I 120 PHE cc_start: 0.9729 (t80) cc_final: 0.9404 (t80) REVERT: I 137 TYR cc_start: 0.7652 (m-10) cc_final: 0.7311 (m-80) REVERT: K 123 TYR cc_start: 0.9867 (t80) cc_final: 0.9652 (t80) REVERT: K 126 TYR cc_start: 0.9322 (m-10) cc_final: 0.9109 (m-80) REVERT: K 127 PHE cc_start: 0.9810 (t80) cc_final: 0.9290 (t80) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 0.1456 time to fit residues: 34.9037 Evaluate side-chains 119 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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: 6.9990 chunk 36 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 187 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 192 optimal weight: 4.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS A 174 HIS ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 HIS ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 306 ASN F 549 ASN H 129 GLN H 177 ASN H 207 GLN I 27 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.044952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.037775 restraints weight = 269887.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.038575 restraints weight = 170022.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.039068 restraints weight = 118330.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.039440 restraints weight = 93812.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.039673 restraints weight = 78737.143| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 17802 Z= 0.278 Angle : 0.732 9.399 24081 Z= 0.397 Chirality : 0.044 0.303 2651 Planarity : 0.004 0.046 2973 Dihedral : 13.551 177.185 2654 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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: -0.63 (0.18), residues: 2022 helix: 0.53 (0.16), residues: 912 sheet: -0.12 (0.27), residues: 387 loop : -1.76 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 405 TYR 0.021 0.002 TYR C 206 PHE 0.069 0.003 PHE I 85 TRP 0.025 0.002 TRP F 339 HIS 0.009 0.002 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.28 (17801) covalent geometry : angle 0.73143 / 0.40 (24079) SS BOND : bond 0.01266 / 0.67 ( 1) SS BOND : angle 3.08213 / 1.66 ( 2) hydrogen bonds : bond 0.04523 / 3.14 ( 800) hydrogen bonds : angle 5.37119 / 3.66 ( 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 149 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.701 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: B 115 ASP cc_start: 0.9622 (t0) cc_final: 0.9066 (m-30) REVERT: C 55 MET cc_start: 0.9463 (tpt) cc_final: 0.9216 (tpt) REVERT: E 24 MET cc_start: 0.7895 (ttt) cc_final: 0.6430 (ppp) REVERT: E 51 LYS cc_start: 0.9188 (mmpt) cc_final: 0.8871 (mmmt) REVERT: E 116 LEU cc_start: 0.9632 (tp) cc_final: 0.8876 (tp) REVERT: E 119 MET cc_start: 0.8837 (mmt) cc_final: 0.8546 (mmp) REVERT: E 129 LEU cc_start: 0.9891 (mt) cc_final: 0.9674 (tp) REVERT: F 160 MET cc_start: 0.9071 (mmp) cc_final: 0.8808 (mmm) REVERT: F 189 TRP cc_start: 0.9330 (m-10) cc_final: 0.9093 (m-10) REVERT: F 420 ASP cc_start: 0.9659 (m-30) cc_final: 0.9136 (t0) REVERT: F 496 MET cc_start: 0.7048 (ppp) cc_final: 0.6626 (pmm) REVERT: F 588 LEU cc_start: 0.9918 (tp) cc_final: 0.9688 (mm) REVERT: F 589 PHE cc_start: 0.9716 (t80) cc_final: 0.9433 (t80) REVERT: H 28 MET cc_start: 0.9645 (mtp) cc_final: 0.9424 (ttt) REVERT: H 184 TYR cc_start: 0.9335 (m-80) cc_final: 0.8984 (m-80) REVERT: H 226 MET cc_start: 0.8748 (mmm) cc_final: 0.8425 (mmm) REVERT: I 86 TYR cc_start: 0.8981 (m-80) cc_final: 0.8769 (m-80) REVERT: I 120 PHE cc_start: 0.9700 (t80) cc_final: 0.9407 (t80) REVERT: K 45 THR cc_start: 0.9090 (p) cc_final: 0.8388 (p) REVERT: K 52 MET cc_start: 0.9852 (ptp) cc_final: 0.9441 (tpt) REVERT: K 86 TYR cc_start: 0.9687 (m-10) cc_final: 0.9397 (m-10) REVERT: K 123 TYR cc_start: 0.9868 (t80) cc_final: 0.9534 (t80) REVERT: K 126 TYR cc_start: 0.9264 (m-10) cc_final: 0.9040 (m-80) REVERT: K 127 PHE cc_start: 0.9815 (t80) cc_final: 0.9045 (t80) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1483 time to fit residues: 33.7387 Evaluate side-chains 115 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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: 0.2980 chunk 21 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 0.2980 chunk 202 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 85 optimal weight: 0.0070 chunk 141 optimal weight: 7.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 155 ASN C 168 ASN E 324 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS F 560 GLN F 681 GLN K 41 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.047068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.039950 restraints weight = 257312.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.040759 restraints weight = 155240.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.041367 restraints weight = 109764.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.041738 restraints weight = 83218.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.042011 restraints weight = 69071.439| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17802 Z= 0.113 Angle : 0.570 8.555 24081 Z= 0.305 Chirality : 0.042 0.223 2651 Planarity : 0.003 0.037 2973 Dihedral : 13.350 176.231 2654 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.05 % Allowed : 1.84 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.18), residues: 2022 helix: 0.86 (0.17), residues: 917 sheet: 0.16 (0.27), residues: 371 loop : -1.59 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 246 TYR 0.023 0.001 TYR H 255 PHE 0.048 0.002 PHE I 85 TRP 0.026 0.002 TRP H 52 HIS 0.006 0.001 HIS F 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (17801) covalent geometry : angle 0.56939 / 0.30 (24079) SS BOND : bond 0.00123 / 0.06 ( 1) SS BOND : angle 1.93436 / 1.06 ( 2) hydrogen bonds : bond 0.03697 / 2.57 ( 800) hydrogen bonds : angle 5.05798 / 3.48 ( 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 145 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.704 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: A 55 MET cc_start: 0.9623 (mmt) cc_final: 0.9300 (mmp) REVERT: B 55 MET cc_start: 0.9621 (mmp) cc_final: 0.9392 (mmm) REVERT: B 115 ASP cc_start: 0.9509 (t0) cc_final: 0.8923 (m-30) REVERT: C 55 MET cc_start: 0.9462 (tpt) cc_final: 0.9179 (tpt) REVERT: E 24 MET cc_start: 0.7670 (ttt) cc_final: 0.6233 (ppp) REVERT: E 49 PHE cc_start: 0.9650 (t80) cc_final: 0.9425 (t80) REVERT: E 51 LYS cc_start: 0.9172 (mmpt) cc_final: 0.8930 (mmmt) REVERT: E 56 LEU cc_start: 0.8988 (tp) cc_final: 0.8702 (tp) REVERT: E 116 LEU cc_start: 0.9622 (tp) cc_final: 0.8915 (tp) REVERT: E 119 MET cc_start: 0.9137 (mmt) cc_final: 0.8897 (mmp) REVERT: F 8 MET cc_start: 0.9739 (mmp) cc_final: 0.9533 (mmm) REVERT: F 47 PHE cc_start: 0.7831 (m-80) cc_final: 0.7225 (m-80) REVERT: F 160 MET cc_start: 0.8952 (mmp) cc_final: 0.8705 (mmm) REVERT: F 189 TRP cc_start: 0.9264 (m-10) cc_final: 0.9025 (m-10) REVERT: F 363 MET cc_start: 0.7724 (mmm) cc_final: 0.7326 (mmm) REVERT: F 420 ASP cc_start: 0.9660 (m-30) cc_final: 0.9116 (t0) REVERT: F 496 MET cc_start: 0.7642 (ppp) cc_final: 0.7367 (pmm) REVERT: F 588 LEU cc_start: 0.9917 (tp) cc_final: 0.9704 (mm) REVERT: F 589 PHE cc_start: 0.9709 (t80) cc_final: 0.9293 (t80) REVERT: F 624 MET cc_start: 0.7541 (mmm) cc_final: 0.7145 (mpp) REVERT: H 28 MET cc_start: 0.9666 (mtp) cc_final: 0.9440 (ttt) REVERT: H 184 TYR cc_start: 0.9229 (m-80) cc_final: 0.8814 (m-80) REVERT: H 226 MET cc_start: 0.8622 (mmm) cc_final: 0.8264 (mmm) REVERT: I 86 TYR cc_start: 0.8865 (m-80) cc_final: 0.8646 (m-80) REVERT: I 120 PHE cc_start: 0.9674 (t80) cc_final: 0.9378 (t80) REVERT: K 45 THR cc_start: 0.8962 (p) cc_final: 0.8268 (p) REVERT: K 52 MET cc_start: 0.9849 (ptp) cc_final: 0.9453 (tpt) REVERT: K 86 TYR cc_start: 0.9655 (m-10) cc_final: 0.9389 (m-80) REVERT: K 123 TYR cc_start: 0.9876 (t80) cc_final: 0.9460 (t80) REVERT: K 126 TYR cc_start: 0.9233 (m-10) cc_final: 0.8987 (m-80) REVERT: K 127 PHE cc_start: 0.9802 (t80) cc_final: 0.9054 (t80) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.1411 time to fit residues: 31.4921 Evaluate side-chains 115 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 6.9990 chunk 123 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 HIS ** H 197 GLN ** 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 = 0.3125 r_free = 0.3125 target = 0.044756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037656 restraints weight = 266894.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.038433 restraints weight = 166646.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.038934 restraints weight = 116183.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.039314 restraints weight = 91534.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.039563 restraints weight = 76022.174| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17802 Z= 0.182 Angle : 0.590 8.409 24081 Z= 0.318 Chirality : 0.041 0.173 2651 Planarity : 0.003 0.037 2973 Dihedral : 13.251 176.623 2654 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: -0.15 (0.18), residues: 2022 helix: 1.01 (0.17), residues: 905 sheet: 0.05 (0.27), residues: 384 loop : -1.58 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 110 TYR 0.024 0.002 TYR F 479 PHE 0.026 0.002 PHE I 40 TRP 0.020 0.002 TRP F 339 HIS 0.006 0.001 HIS H 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (17801) covalent geometry : angle 0.58979 / 0.32 (24079) SS BOND : bond 0.00227 / 0.12 ( 1) SS BOND : angle 1.23932 / 0.69 ( 2) hydrogen bonds : bond 0.03834 / 2.67 ( 800) hydrogen bonds : angle 5.02530 / 3.45 ( 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 134 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.9600 (mmp) cc_final: 0.9390 (mmm) REVERT: B 115 ASP cc_start: 0.9446 (t0) cc_final: 0.9241 (m-30) REVERT: C 55 MET cc_start: 0.9444 (tpt) cc_final: 0.9181 (tpt) REVERT: E 24 MET cc_start: 0.7781 (ttt) cc_final: 0.6346 (ppp) REVERT: E 51 LYS cc_start: 0.9178 (mmpt) cc_final: 0.8929 (mmmt) REVERT: E 56 LEU cc_start: 0.8970 (tp) cc_final: 0.8653 (tp) REVERT: E 62 PHE cc_start: 0.9265 (m-10) cc_final: 0.9061 (m-10) REVERT: F 363 MET cc_start: 0.7849 (mmm) cc_final: 0.7365 (mmm) REVERT: F 420 ASP cc_start: 0.9669 (m-30) cc_final: 0.9078 (t0) REVERT: F 588 LEU cc_start: 0.9916 (tp) cc_final: 0.9690 (mm) REVERT: F 589 PHE cc_start: 0.9705 (t80) cc_final: 0.9289 (t80) REVERT: F 624 MET cc_start: 0.7927 (mmm) cc_final: 0.7391 (mpp) REVERT: H 28 MET cc_start: 0.9669 (mtp) cc_final: 0.9423 (ttt) REVERT: H 184 TYR cc_start: 0.9166 (m-80) cc_final: 0.8868 (m-80) REVERT: H 226 MET cc_start: 0.8649 (mmm) cc_final: 0.8441 (mmm) REVERT: I 120 PHE cc_start: 0.9472 (t80) cc_final: 0.9105 (t80) REVERT: K 86 TYR cc_start: 0.9683 (m-10) cc_final: 0.9337 (m-80) REVERT: K 123 TYR cc_start: 0.9867 (t80) cc_final: 0.9576 (t80) REVERT: K 126 TYR cc_start: 0.9237 (m-10) cc_final: 0.9011 (m-80) REVERT: K 127 PHE cc_start: 0.9816 (t80) cc_final: 0.9268 (t80) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1488 time to fit residues: 30.2277 Evaluate side-chains 106 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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: 0.4980 chunk 177 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 chunk 108 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** 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 = 0.3110 r_free = 0.3110 target = 0.044025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.037039 restraints weight = 269833.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.037812 restraints weight = 166406.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.038319 restraints weight = 116787.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.038710 restraints weight = 91064.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.038922 restraints weight = 74784.287| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17802 Z= 0.170 Angle : 0.597 7.885 24081 Z= 0.323 Chirality : 0.042 0.344 2651 Planarity : 0.003 0.044 2973 Dihedral : 13.182 176.656 2654 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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: -0.14 (0.18), residues: 2022 helix: 0.96 (0.17), residues: 915 sheet: 0.06 (0.28), residues: 367 loop : -1.48 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 110 TYR 0.028 0.002 TYR I 86 PHE 0.036 0.002 PHE K 85 TRP 0.017 0.001 TRP F 339 HIS 0.005 0.001 HIS F 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (17801) covalent geometry : angle 0.59641 / 0.32 (24079) SS BOND : bond 0.00628 / 0.33 ( 1) SS BOND : angle 1.33177 / 0.73 ( 2) hydrogen bonds : bond 0.03826 / 2.65 ( 800) hydrogen bonds : angle 5.07171 / 3.49 ( 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 131 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.725 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: A 55 MET cc_start: 0.9642 (mmt) cc_final: 0.9376 (mmp) REVERT: B 115 ASP cc_start: 0.9468 (t0) cc_final: 0.9247 (m-30) REVERT: C 55 MET cc_start: 0.9459 (tpt) cc_final: 0.9144 (tpt) REVERT: E 24 MET cc_start: 0.7716 (ttt) cc_final: 0.6285 (ppp) REVERT: E 49 PHE cc_start: 0.9641 (t80) cc_final: 0.9290 (t80) REVERT: E 51 LYS cc_start: 0.9160 (mmpt) cc_final: 0.8948 (mmmt) REVERT: E 56 LEU cc_start: 0.8961 (tp) cc_final: 0.8690 (tp) REVERT: F 363 MET cc_start: 0.7870 (mmm) cc_final: 0.7414 (mmm) REVERT: F 420 ASP cc_start: 0.9615 (m-30) cc_final: 0.8877 (t0) REVERT: F 496 MET cc_start: 0.5187 (pmm) cc_final: 0.4729 (pmm) REVERT: F 588 LEU cc_start: 0.9901 (tp) cc_final: 0.9630 (mm) REVERT: F 589 PHE cc_start: 0.9741 (t80) cc_final: 0.9327 (t80) REVERT: F 624 MET cc_start: 0.7937 (mmm) cc_final: 0.7491 (mpp) REVERT: H 28 MET cc_start: 0.9690 (mtp) cc_final: 0.9394 (ttt) REVERT: H 184 TYR cc_start: 0.9373 (m-80) cc_final: 0.8986 (m-80) REVERT: H 226 MET cc_start: 0.8613 (mmm) cc_final: 0.8396 (mmm) REVERT: I 120 PHE cc_start: 0.9606 (t80) cc_final: 0.9325 (t80) REVERT: K 83 ILE cc_start: 0.9563 (mm) cc_final: 0.9079 (mm) REVERT: K 86 TYR cc_start: 0.9675 (m-10) cc_final: 0.9351 (m-80) REVERT: K 123 TYR cc_start: 0.9884 (t80) cc_final: 0.9392 (t80) REVERT: K 126 TYR cc_start: 0.9230 (m-10) cc_final: 0.8985 (m-80) REVERT: K 127 PHE cc_start: 0.9832 (t80) cc_final: 0.9218 (t80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1489 time to fit residues: 29.7316 Evaluate side-chains 106 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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: 0.6980 chunk 158 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 106 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 324 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.044671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.037658 restraints weight = 265487.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.038466 restraints weight = 161819.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.039030 restraints weight = 112360.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.039394 restraints weight = 84942.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.039622 restraints weight = 70730.956| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17802 Z= 0.116 Angle : 0.541 7.756 24081 Z= 0.291 Chirality : 0.041 0.263 2651 Planarity : 0.003 0.039 2973 Dihedral : 13.064 176.314 2654 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.05 % Allowed : 0.54 % Favored : 99.41 % 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: 1.09 (0.17), residues: 910 sheet: 0.11 (0.28), residues: 364 loop : -1.46 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 52 TYR 0.050 0.001 TYR I 86 PHE 0.036 0.002 PHE I 105 TRP 0.014 0.001 TRP F 339 HIS 0.004 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (17801) covalent geometry : angle 0.54083 / 0.29 (24079) SS BOND : bond 0.00264 / 0.14 ( 1) SS BOND : angle 1.15858 / 0.64 ( 2) hydrogen bonds : bond 0.03528 / 2.44 ( 800) hydrogen bonds : angle 4.92913 / 3.39 ( 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 131 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.683 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: 0.9604 (mmt) cc_final: 0.9351 (mmp) REVERT: C 55 MET cc_start: 0.9470 (tpt) cc_final: 0.9150 (tpt) REVERT: E 24 MET cc_start: 0.7979 (ttt) cc_final: 0.7257 (ppp) REVERT: E 49 PHE cc_start: 0.9715 (t80) cc_final: 0.9403 (t80) REVERT: E 51 LYS cc_start: 0.9176 (mmpt) cc_final: 0.8962 (mmmt) REVERT: E 56 LEU cc_start: 0.8865 (tp) cc_final: 0.8580 (tp) REVERT: F 1 MET cc_start: 0.7711 (tpt) cc_final: 0.7421 (tmm) REVERT: F 8 MET cc_start: 0.9722 (mmp) cc_final: 0.9516 (mmm) REVERT: F 363 MET cc_start: 0.7830 (mmm) cc_final: 0.7374 (mmm) REVERT: F 420 ASP cc_start: 0.9616 (m-30) cc_final: 0.8881 (t0) REVERT: F 496 MET cc_start: 0.5131 (pmm) cc_final: 0.4673 (pmm) REVERT: F 588 LEU cc_start: 0.9913 (tp) cc_final: 0.9699 (mm) REVERT: F 589 PHE cc_start: 0.9742 (t80) cc_final: 0.9363 (t80) REVERT: F 624 MET cc_start: 0.7926 (mmm) cc_final: 0.7520 (mpp) REVERT: H 28 MET cc_start: 0.9710 (mtp) cc_final: 0.9452 (ttt) REVERT: H 184 TYR cc_start: 0.9206 (m-80) cc_final: 0.8890 (m-80) REVERT: H 226 MET cc_start: 0.8551 (mmm) cc_final: 0.8317 (mmm) REVERT: I 120 PHE cc_start: 0.9591 (t80) cc_final: 0.9281 (t80) REVERT: K 54 GLN cc_start: 0.9691 (tp-100) cc_final: 0.9486 (tp-100) REVERT: K 83 ILE cc_start: 0.9502 (mm) cc_final: 0.9099 (mm) REVERT: K 86 TYR cc_start: 0.9677 (m-10) cc_final: 0.9362 (m-80) REVERT: K 123 TYR cc_start: 0.9861 (t80) cc_final: 0.9384 (t80) REVERT: K 126 TYR cc_start: 0.9219 (m-10) cc_final: 0.8964 (m-80) REVERT: K 127 PHE cc_start: 0.9830 (t80) cc_final: 0.9213 (t80) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1404 time to fit residues: 28.3644 Evaluate side-chains 111 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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: 10.0000 chunk 167 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 162 optimal weight: 0.0670 chunk 178 optimal weight: 0.0050 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 overall best weight: 0.7536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.045031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.037957 restraints weight = 265121.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.038778 restraints weight = 161425.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.039277 restraints weight = 113060.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.039687 restraints weight = 88142.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.039952 restraints weight = 71956.564| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17802 Z= 0.107 Angle : 0.538 8.775 24081 Z= 0.288 Chirality : 0.041 0.256 2651 Planarity : 0.003 0.042 2973 Dihedral : 12.949 176.406 2654 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.05 % Allowed : 0.65 % Favored : 99.30 % 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: 1.16 (0.17), residues: 910 sheet: 0.07 (0.28), residues: 372 loop : -1.43 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 22 TYR 0.017 0.001 TYR E 57 PHE 0.013 0.001 PHE E 92 TRP 0.013 0.001 TRP F 339 HIS 0.004 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (17801) covalent geometry : angle 0.53802 / 0.29 (24079) SS BOND : bond 0.00184 / 0.10 ( 1) SS BOND : angle 0.99148 / 0.56 ( 2) hydrogen bonds : bond 0.03455 / 2.39 ( 800) hydrogen bonds : angle 4.84076 / 3.34 ( 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 133 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9637 (mmt) cc_final: 0.9356 (mmp) REVERT: C 55 MET cc_start: 0.9473 (tpt) cc_final: 0.9153 (tpt) REVERT: E 24 MET cc_start: 0.7958 (ttt) cc_final: 0.7271 (ppp) REVERT: E 49 PHE cc_start: 0.9725 (t80) cc_final: 0.9426 (t80) REVERT: E 51 LYS cc_start: 0.8959 (mmpt) cc_final: 0.8708 (mmmt) REVERT: E 56 LEU cc_start: 0.8906 (tp) cc_final: 0.8653 (tp) REVERT: F 1 MET cc_start: 0.7706 (tpt) cc_final: 0.7348 (tmm) REVERT: F 8 MET cc_start: 0.9713 (mmp) cc_final: 0.9507 (mmm) REVERT: F 47 PHE cc_start: 0.7662 (m-80) cc_final: 0.6914 (m-80) REVERT: F 189 TRP cc_start: 0.9564 (m-10) cc_final: 0.9029 (m-10) REVERT: F 363 MET cc_start: 0.7835 (mmm) cc_final: 0.7380 (mmm) REVERT: F 420 ASP cc_start: 0.9610 (m-30) cc_final: 0.8887 (t0) REVERT: F 496 MET cc_start: 0.4992 (pmm) cc_final: 0.4646 (pmm) REVERT: F 588 LEU cc_start: 0.9909 (tp) cc_final: 0.9694 (mm) REVERT: F 589 PHE cc_start: 0.9731 (t80) cc_final: 0.9341 (t80) REVERT: F 624 MET cc_start: 0.7946 (mmm) cc_final: 0.7469 (mpp) REVERT: H 28 MET cc_start: 0.9670 (mtp) cc_final: 0.9408 (ttt) REVERT: H 129 GLN cc_start: 0.9553 (mm110) cc_final: 0.9246 (mp10) REVERT: H 184 TYR cc_start: 0.9162 (m-80) cc_final: 0.8874 (m-80) REVERT: H 226 MET cc_start: 0.8524 (mmm) cc_final: 0.8282 (mmm) REVERT: I 120 PHE cc_start: 0.9593 (t80) cc_final: 0.9295 (t80) REVERT: K 54 GLN cc_start: 0.9692 (tp-100) cc_final: 0.9476 (tp-100) REVERT: K 83 ILE cc_start: 0.9541 (mm) cc_final: 0.9135 (mm) REVERT: K 86 TYR cc_start: 0.9686 (m-10) cc_final: 0.9366 (m-80) REVERT: K 123 TYR cc_start: 0.9853 (t80) cc_final: 0.9365 (t80) REVERT: K 126 TYR cc_start: 0.9210 (m-10) cc_final: 0.8954 (m-80) REVERT: K 127 PHE cc_start: 0.9811 (t80) cc_final: 0.9195 (t80) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.1468 time to fit residues: 30.1695 Evaluate side-chains 113 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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: 4.9990 chunk 134 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 184 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 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** I 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.043384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036432 restraints weight = 272870.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.037109 restraints weight = 170039.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.037711 restraints weight = 121181.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.038074 restraints weight = 91554.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.038238 restraints weight = 75367.260| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17802 Z= 0.182 Angle : 0.602 10.284 24081 Z= 0.325 Chirality : 0.041 0.261 2651 Planarity : 0.004 0.070 2973 Dihedral : 12.945 177.445 2654 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 916 sheet: 0.04 (0.29), residues: 363 loop : -1.43 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 91 TYR 0.045 0.002 TYR I 86 PHE 0.029 0.002 PHE K 85 TRP 0.019 0.002 TRP F 339 HIS 0.005 0.001 HIS F 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (17801) covalent geometry : angle 0.60168 / 0.33 (24079) SS BOND : bond 0.00672 / 0.35 ( 1) SS BOND : angle 0.99356 / 0.54 ( 2) hydrogen bonds : bond 0.03757 / 2.59 ( 800) hydrogen bonds : angle 4.97816 / 3.43 ( 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 : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9608 (mmt) cc_final: 0.9297 (mmp) REVERT: C 55 MET cc_start: 0.9445 (tpt) cc_final: 0.9164 (tpt) REVERT: C 67 MET cc_start: 0.9514 (tmm) cc_final: 0.9256 (tmm) REVERT: E 24 MET cc_start: 0.8039 (ttt) cc_final: 0.7468 (ppp) REVERT: E 49 PHE cc_start: 0.9736 (t80) cc_final: 0.9455 (t80) REVERT: E 56 LEU cc_start: 0.8872 (tp) cc_final: 0.8671 (tp) REVERT: F 189 TRP cc_start: 0.9622 (m-10) cc_final: 0.9160 (m-10) REVERT: F 363 MET cc_start: 0.7989 (mmm) cc_final: 0.7524 (mmm) REVERT: F 420 ASP cc_start: 0.9627 (m-30) cc_final: 0.8823 (t0) REVERT: F 588 LEU cc_start: 0.9906 (tp) cc_final: 0.9653 (mm) REVERT: F 589 PHE cc_start: 0.9773 (t80) cc_final: 0.9439 (t80) REVERT: F 624 MET cc_start: 0.8077 (mmm) cc_final: 0.7544 (mpp) REVERT: H 28 MET cc_start: 0.9694 (mtp) cc_final: 0.9383 (ttt) REVERT: H 184 TYR cc_start: 0.9188 (m-80) cc_final: 0.8897 (m-80) REVERT: H 226 MET cc_start: 0.8637 (mmm) cc_final: 0.8381 (mmm) REVERT: I 54 GLN cc_start: 0.9060 (mp10) cc_final: 0.8753 (mp10) REVERT: I 120 PHE cc_start: 0.9601 (t80) cc_final: 0.9342 (t80) REVERT: K 83 ILE cc_start: 0.9488 (mm) cc_final: 0.9078 (mm) REVERT: K 86 TYR cc_start: 0.9686 (m-10) cc_final: 0.9388 (m-80) REVERT: K 123 TYR cc_start: 0.9829 (t80) cc_final: 0.9359 (t80) REVERT: K 126 TYR cc_start: 0.9231 (m-10) cc_final: 0.8984 (m-80) REVERT: K 127 PHE cc_start: 0.9810 (t80) cc_final: 0.9239 (t80) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1461 time to fit residues: 28.0294 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 : 0.839 ------------------------------------------------------------------------------- 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: 0.8980 chunk 188 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 324 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.044059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.037008 restraints weight = 269935.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.037766 restraints weight = 166933.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.038347 restraints weight = 117740.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.038735 restraints weight = 88628.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.038988 restraints weight = 72382.014| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17802 Z= 0.115 Angle : 0.548 9.859 24081 Z= 0.291 Chirality : 0.041 0.248 2651 Planarity : 0.003 0.057 2973 Dihedral : 12.889 177.066 2654 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.05 % Allowed : 0.27 % Favored : 99.68 % 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: 0.00 (0.19), residues: 2022 helix: 1.15 (0.17), residues: 910 sheet: 0.02 (0.28), residues: 365 loop : -1.43 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 110 TYR 0.051 0.001 TYR I 86 PHE 0.017 0.001 PHE I 105 TRP 0.055 0.002 TRP H 52 HIS 0.004 0.001 HIS H 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (17801) covalent geometry : angle 0.54753 / 0.29 (24079) SS BOND : bond 0.00279 / 0.15 ( 1) SS BOND : angle 1.18694 / 0.66 ( 2) hydrogen bonds : bond 0.03431 / 2.37 ( 800) hydrogen bonds : angle 4.86423 / 3.35 ( 2325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2541.33 seconds wall clock time: 45 minutes 23.13 seconds (2723.13 seconds total)