Starting phenix.real_space_refine on Sat Jul 4 02:30:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v02_26927/07_2026/7v02_26927_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v02_26927/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7v02_26927/07_2026/7v02_26927_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v02_26927/07_2026/7v02_26927_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v02_26927/07_2026/7v02_26927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v02_26927/07_2026/7v02_26927.map" } resolution = 4.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 29 5.49 5 S 49 5.16 5 C 10999 2.51 5 N 2928 2.21 5 O 3412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 4.10, 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: 1.66 Conformation dependent library (CDL) restraints added in 815.9 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: 2.70 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: 3.36 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5494 1.34 - 1.46: 4089 1.46 - 1.58: 8075 1.58 - 1.70: 57 1.70 - 1.82: 86 Bond restraints: 17801 Sorted by residual: bond pdb=" O3' U G 22 " pdb=" P A G 23 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.17e+01 bond pdb=" C3' U G 24 " pdb=" O3' U G 24 " ideal model delta sigma weight residual 1.417 1.466 -0.049 1.50e-02 4.44e+03 1.07e+01 bond pdb=" N ILE F 120 " pdb=" CA ILE F 120 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.04e+01 bond pdb=" N ILE A 91 " pdb=" CA ILE A 91 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.65e+00 bond pdb=" N ASP E 122 " pdb=" CA ASP E 122 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.14e-02 7.69e+03 9.46e+00 ... (remaining 17796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 23405 2.54 - 5.08: 580 5.08 - 7.61: 80 7.61 - 10.15: 10 10.15 - 12.69: 4 Bond angle restraints: 24079 Sorted by residual: angle pdb=" C4' A G 27 " pdb=" C3' A G 27 " pdb=" O3' A G 27 " ideal model delta sigma weight residual 109.40 96.71 12.69 1.50e+00 4.44e-01 7.16e+01 angle pdb=" C3' C G 8 " pdb=" O3' C G 8 " pdb=" P A G 9 " ideal model delta sigma weight residual 120.20 130.50 -10.30 1.50e+00 4.44e-01 4.71e+01 angle pdb=" CA ASP E 122 " pdb=" CB ASP E 122 " pdb=" CG ASP E 122 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.00e+00 1.00e+00 3.12e+01 angle pdb=" C4' A G 19 " pdb=" C3' A G 19 " pdb=" O3' A G 19 " ideal model delta sigma weight residual 113.00 121.30 -8.30 1.50e+00 4.44e-01 3.06e+01 angle pdb=" N1 C G 10 " pdb=" C2 C G 10 " pdb=" O2 C G 10 " ideal model delta sigma weight residual 118.90 122.18 -3.28 6.00e-01 2.78e+00 2.99e+01 ... (remaining 24074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 10487 35.89 - 71.79: 195 71.79 - 107.68: 20 107.68 - 143.58: 2 143.58 - 179.47: 2 Dihedral angle restraints: 10706 sinusoidal: 4667 harmonic: 6039 Sorted by residual: dihedral pdb=" O4' C G 10 " pdb=" C1' C G 10 " pdb=" N1 C G 10 " pdb=" C2 C G 10 " ideal model delta sinusoidal sigma weight residual -160.00 -2.54 -157.46 1 1.50e+01 4.44e-03 8.21e+01 dihedral pdb=" CB CYS F 410 " pdb=" SG CYS F 410 " pdb=" SG CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sinusoidal sigma weight residual -86.00 -158.19 72.19 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual 232.00 52.53 179.47 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 10703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2093 0.066 - 0.132: 466 0.132 - 0.198: 67 0.198 - 0.264: 19 0.264 - 0.330: 6 Chirality restraints: 2651 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" P G G 5 " pdb=" OP1 G G 5 " pdb=" OP2 G G 5 " pdb=" O5' G G 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE C 91 " pdb=" CA ILE C 91 " pdb=" CG1 ILE C 91 " pdb=" CG2 ILE C 91 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2648 not shown) Planarity restraints: 2973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 339 " -0.031 2.00e-02 2.50e+03 3.09e-02 2.39e+01 pdb=" CG TRP F 339 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP F 339 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP F 339 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 339 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP F 339 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 339 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 339 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 339 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP F 339 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 85 " -0.022 2.00e-02 2.50e+03 2.21e-02 8.51e+00 pdb=" CG PHE I 85 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE I 85 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE I 85 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE I 85 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE I 85 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE I 85 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 72 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" CG ASP F 72 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP F 72 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP F 72 " -0.014 2.00e-02 2.50e+03 ... (remaining 2970 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 152 2.62 - 3.19: 15977 3.19 - 3.76: 25525 3.76 - 4.33: 36218 4.33 - 4.90: 58169 Nonbonded interactions: 136041 Sorted by model distance: nonbonded pdb=" O ARG A 144 " pdb=" OE1 GLN C 40 " model vdw 2.048 3.040 nonbonded pdb=" O LEU E 55 " pdb=" OG1 THR E 58 " model vdw 2.098 3.040 nonbonded pdb=" NH2 ARG A 129 " pdb=" OD1 ASN C 57 " model vdw 2.158 3.120 nonbonded pdb=" O PHE F 344 " pdb=" OG1 THR F 345 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR F 499 " pdb=" O GLU F 574 " model vdw 2.265 3.040 ... (remaining 136036 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 21 \ 4)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 21 \ 4)) } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.920 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.220 ------------------------------------------------------------------------------- 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= 0.359 Angle : 0.931 12.691 24081 Z= 0.562 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 0.00609 / 0.36 (17801) covalent geometry : angle 0.93108 / 0.56 (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 : 0.709 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: 0.1598 time to fit residues: 67.3863 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 : 0.651 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 708 ASN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.050729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.043378 restraints weight = 248398.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.044222 restraints weight = 154348.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.044857 restraints weight = 109847.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.045291 restraints weight = 82904.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.045538 restraints weight = 67697.746| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17802 Z= 0.199 Angle : 0.713 10.510 24081 Z= 0.390 Chirality : 0.046 0.221 2651 Planarity : 0.004 0.036 2973 Dihedral : 13.820 176.169 2654 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.16 % Allowed : 2.59 % Favored : 97.24 % 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: -0.61 (0.18), residues: 2022 helix: 0.59 (0.17), residues: 913 sheet: -0.02 (0.27), residues: 369 loop : -1.84 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 81 TYR 0.024 0.002 TYR H 104 PHE 0.032 0.002 PHE I 85 TRP 0.038 0.002 TRP F 339 HIS 0.018 0.002 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 (17801) covalent geometry : angle 0.71278 / 0.39 (24079) SS BOND : bond 0.00266 / 0.14 ( 1) SS BOND : angle 0.83170 / 0.47 ( 2) hydrogen bonds : bond 0.05096 / 3.54 ( 800) hydrogen bonds : angle 5.63028 / 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 : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LEU cc_start: 0.9844 (tt) cc_final: 0.9189 (mt) REVERT: B 115 ASP cc_start: 0.9640 (t0) cc_final: 0.8977 (m-30) REVERT: C 55 MET cc_start: 0.9548 (tpt) cc_final: 0.9231 (tpt) REVERT: E 49 PHE cc_start: 0.9482 (t80) cc_final: 0.9218 (t80) REVERT: F 163 MET cc_start: 0.9440 (ptp) cc_final: 0.9195 (ptp) REVERT: F 496 MET cc_start: 0.6735 (ppp) cc_final: 0.5686 (pmm) REVERT: F 588 LEU cc_start: 0.9961 (tp) cc_final: 0.9752 (mm) REVERT: F 589 PHE cc_start: 0.9674 (t80) cc_final: 0.9289 (t80) REVERT: F 665 ASP cc_start: 0.9894 (p0) cc_final: 0.9689 (p0) REVERT: I 85 PHE cc_start: 0.9568 (m-80) cc_final: 0.9363 (m-80) REVERT: I 86 TYR cc_start: 0.8960 (m-80) cc_final: 0.8596 (m-80) REVERT: I 120 PHE cc_start: 0.9537 (t80) cc_final: 0.9246 (t80) REVERT: I 137 TYR cc_start: 0.7516 (m-10) cc_final: 0.7207 (m-80) REVERT: K 27 ASN cc_start: 0.7221 (OUTLIER) cc_final: 0.6752 (m-40) REVERT: K 83 ILE cc_start: 0.9639 (mm) cc_final: 0.9309 (mm) REVERT: K 86 TYR cc_start: 0.9722 (m-10) cc_final: 0.9352 (m-80) REVERT: K 126 TYR cc_start: 0.9265 (m-10) cc_final: 0.9051 (m-80) REVERT: K 127 PHE cc_start: 0.9874 (t80) cc_final: 0.9400 (t80) outliers start: 3 outliers final: 0 residues processed: 179 average time/residue: 0.1313 time to fit residues: 35.6571 Evaluate side-chains 129 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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: 0.0030 chunk 1 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.049736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.042385 restraints weight = 253265.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.043265 restraints weight = 157617.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.043804 restraints weight = 110729.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.044262 restraints weight = 86861.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.044517 restraints weight = 71225.567| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17802 Z= 0.156 Angle : 0.613 10.333 24081 Z= 0.334 Chirality : 0.043 0.212 2651 Planarity : 0.003 0.041 2973 Dihedral : 13.590 175.152 2654 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.11 % Allowed : 2.32 % Favored : 97.57 % 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: -0.42 (0.18), residues: 2022 helix: 0.76 (0.17), residues: 916 sheet: -0.04 (0.26), residues: 377 loop : -1.72 (0.21), residues: 729 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 0.033 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 0.00312 / 0.16 (17801) covalent geometry : angle 0.61206 / 0.33 (24079) SS BOND : bond 0.00120 / 0.06 ( 1) SS BOND : angle 3.40537 / 1.88 ( 2) hydrogen bonds : bond 0.04363 / 3.00 ( 800) hydrogen bonds : angle 5.27699 / 3.62 ( 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 155 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.707 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: A 17 LEU cc_start: 0.9929 (tp) cc_final: 0.9340 (mp) REVERT: A 55 MET cc_start: 0.9687 (mmt) cc_final: 0.9479 (mmp) REVERT: B 17 LEU cc_start: 0.9846 (tt) cc_final: 0.9166 (mt) REVERT: B 115 ASP cc_start: 0.9657 (t0) cc_final: 0.8997 (m-30) REVERT: C 55 MET cc_start: 0.9513 (tpt) cc_final: 0.9189 (tpt) REVERT: E 24 MET cc_start: 0.6937 (ttt) cc_final: 0.6099 (tpp) REVERT: E 49 PHE cc_start: 0.9623 (t80) cc_final: 0.9381 (t80) REVERT: F 163 MET cc_start: 0.9353 (ptp) cc_final: 0.9111 (ptp) REVERT: F 318 LEU cc_start: 0.9853 (tp) cc_final: 0.9504 (pp) REVERT: F 363 MET cc_start: 0.6569 (mmm) cc_final: 0.6365 (tpt) REVERT: F 496 MET cc_start: 0.6646 (ppp) cc_final: 0.6153 (pmm) REVERT: F 588 LEU cc_start: 0.9926 (tp) cc_final: 0.9703 (mm) REVERT: F 589 PHE cc_start: 0.9677 (t80) cc_final: 0.9270 (t80) REVERT: H 28 MET cc_start: 0.9567 (mtp) cc_final: 0.9363 (ttt) REVERT: H 226 MET cc_start: 0.8779 (mmm) cc_final: 0.8499 (mmm) REVERT: I 86 TYR cc_start: 0.9057 (m-80) cc_final: 0.8829 (m-80) REVERT: I 120 PHE cc_start: 0.9733 (t80) cc_final: 0.9401 (t80) REVERT: I 137 TYR cc_start: 0.7678 (m-10) cc_final: 0.7333 (m-80) REVERT: K 54 GLN cc_start: 0.9663 (tp-100) cc_final: 0.9436 (tp-100) REVERT: K 123 TYR cc_start: 0.9857 (t80) cc_final: 0.9611 (t80) REVERT: K 126 TYR cc_start: 0.9260 (m-10) cc_final: 0.9035 (m-80) REVERT: K 127 PHE cc_start: 0.9813 (t80) cc_final: 0.9251 (t80) outliers start: 2 outliers final: 0 residues processed: 155 average time/residue: 0.1379 time to fit residues: 32.5956 Evaluate side-chains 120 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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: 3.9990 chunk 36 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 60 optimal weight: 0.0770 chunk 99 optimal weight: 0.6980 chunk 192 optimal weight: 6.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 155 ASN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.048964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.041654 restraints weight = 254920.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.042550 restraints weight = 157510.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.043106 restraints weight = 108896.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.043467 restraints weight = 84994.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.043777 restraints weight = 71275.618| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17802 Z= 0.137 Angle : 0.574 12.223 24081 Z= 0.310 Chirality : 0.042 0.278 2651 Planarity : 0.003 0.036 2973 Dihedral : 13.460 175.318 2654 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -0.21 (0.18), residues: 2022 helix: 0.93 (0.17), residues: 913 sheet: 0.03 (0.27), residues: 379 loop : -1.58 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 559 TYR 0.017 0.001 TYR I 87 PHE 0.062 0.002 PHE I 85 TRP 0.018 0.001 TRP F 339 HIS 0.007 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (17801) covalent geometry : angle 0.57351 / 0.31 (24079) SS BOND : bond 0.00317 / 0.17 ( 1) SS BOND : angle 1.99957 / 1.10 ( 2) hydrogen bonds : bond 0.03895 / 2.68 ( 800) hydrogen bonds : angle 5.06212 / 3.46 ( 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 144 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.582 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: B 115 ASP cc_start: 0.9676 (t0) cc_final: 0.9007 (m-30) REVERT: C 55 MET cc_start: 0.9499 (tpt) cc_final: 0.9204 (tpt) REVERT: E 24 MET cc_start: 0.6993 (ttt) cc_final: 0.6200 (tpp) REVERT: E 49 PHE cc_start: 0.9628 (t80) cc_final: 0.9415 (t80) REVERT: E 51 LYS cc_start: 0.9190 (mmpt) cc_final: 0.8954 (mmmt) REVERT: F 189 TRP cc_start: 0.9191 (m-10) cc_final: 0.8986 (m-10) REVERT: F 318 LEU cc_start: 0.9851 (tp) cc_final: 0.9492 (pp) REVERT: F 363 MET cc_start: 0.6642 (mmm) cc_final: 0.6415 (mmm) REVERT: F 420 ASP cc_start: 0.9610 (m-30) cc_final: 0.9053 (t0) REVERT: F 496 MET cc_start: 0.6714 (ppp) cc_final: 0.6315 (pmm) REVERT: F 589 PHE cc_start: 0.9679 (t80) cc_final: 0.9292 (t80) REVERT: H 28 MET cc_start: 0.9586 (mtp) cc_final: 0.9374 (ttt) REVERT: H 129 GLN cc_start: 0.9709 (mm-40) cc_final: 0.9315 (mp10) REVERT: H 226 MET cc_start: 0.8680 (mmm) cc_final: 0.8333 (mmm) REVERT: I 86 TYR cc_start: 0.8977 (m-80) cc_final: 0.8633 (m-80) REVERT: I 120 PHE cc_start: 0.9700 (t80) cc_final: 0.9409 (t80) REVERT: K 45 THR cc_start: 0.9056 (p) cc_final: 0.8525 (p) REVERT: K 52 MET cc_start: 0.9846 (ptp) cc_final: 0.9423 (tpt) REVERT: K 86 TYR cc_start: 0.9670 (m-10) cc_final: 0.9372 (m-10) REVERT: K 123 TYR cc_start: 0.9875 (t80) cc_final: 0.9603 (t80) REVERT: K 126 TYR cc_start: 0.9311 (m-10) cc_final: 0.9092 (m-80) REVERT: K 127 PHE cc_start: 0.9800 (t80) cc_final: 0.9021 (t80) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1345 time to fit residues: 29.7992 Evaluate side-chains 117 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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: 1.9990 chunk 21 optimal weight: 3.9990 chunk 95 optimal weight: 0.0670 chunk 178 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 85 optimal weight: 0.0770 chunk 141 optimal weight: 4.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 155 ASN E 320 HIS 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 306 ASN F 549 ASN F 560 GLN H 207 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.047614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.040381 restraints weight = 258238.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.041214 restraints weight = 159666.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.041764 restraints weight = 111854.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.042200 restraints weight = 86895.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.042451 restraints weight = 72362.906| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17802 Z= 0.144 Angle : 0.562 9.550 24081 Z= 0.304 Chirality : 0.041 0.188 2651 Planarity : 0.003 0.036 2973 Dihedral : 13.346 175.851 2654 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.05 % Allowed : 1.89 % Favored : 98.05 % 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 (0.19), residues: 2022 helix: 1.12 (0.17), residues: 902 sheet: 0.09 (0.27), residues: 379 loop : -1.55 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 553 TYR 0.022 0.001 TYR H 184 PHE 0.029 0.002 PHE I 40 TRP 0.017 0.001 TRP F 339 HIS 0.005 0.001 HIS F 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (17801) covalent geometry : angle 0.56180 / 0.30 (24079) SS BOND : bond 0.00730 / 0.38 ( 1) SS BOND : angle 2.26021 / 1.24 ( 2) hydrogen bonds : bond 0.03746 / 2.59 ( 800) hydrogen bonds : angle 4.99007 / 3.41 ( 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 146 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.715 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 17 LEU cc_start: 0.9932 (tp) cc_final: 0.9610 (mp) REVERT: A 55 MET cc_start: 0.9648 (mmp) cc_final: 0.9441 (mmm) REVERT: B 115 ASP cc_start: 0.9482 (t0) cc_final: 0.8906 (m-30) REVERT: C 55 MET cc_start: 0.9477 (tpt) cc_final: 0.9172 (tpt) REVERT: E 24 MET cc_start: 0.7705 (ttt) cc_final: 0.6173 (ppp) REVERT: E 116 LEU cc_start: 0.9673 (tp) cc_final: 0.8885 (tp) REVERT: E 119 MET cc_start: 0.8930 (mmt) cc_final: 0.8254 (mmm) REVERT: F 160 MET cc_start: 0.8990 (mmp) cc_final: 0.8776 (mmm) REVERT: F 189 TRP cc_start: 0.9212 (m-10) cc_final: 0.8967 (m-10) REVERT: F 363 MET cc_start: 0.9194 (mmm) cc_final: 0.8553 (mmm) REVERT: F 420 ASP cc_start: 0.9643 (m-30) cc_final: 0.9118 (t0) REVERT: F 589 PHE cc_start: 0.9642 (t80) cc_final: 0.9392 (t80) REVERT: F 624 MET cc_start: 0.7844 (mmm) cc_final: 0.7489 (mpp) REVERT: H 28 MET cc_start: 0.9609 (mtp) cc_final: 0.9401 (ttt) REVERT: H 226 MET cc_start: 0.8715 (mmm) cc_final: 0.8334 (mmm) REVERT: I 85 PHE cc_start: 0.9695 (m-10) cc_final: 0.9493 (m-10) REVERT: I 120 PHE cc_start: 0.9689 (t80) cc_final: 0.9405 (t80) REVERT: K 86 TYR cc_start: 0.9685 (m-10) cc_final: 0.9426 (m-80) REVERT: K 126 TYR cc_start: 0.9297 (m-10) cc_final: 0.9088 (m-80) REVERT: K 127 PHE cc_start: 0.9800 (t80) cc_final: 0.9326 (t80) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.1422 time to fit residues: 31.8429 Evaluate side-chains 116 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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: 0.9980 chunk 11 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 35 optimal weight: 0.4980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.047195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.039951 restraints weight = 257447.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.040787 restraints weight = 160968.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.041306 restraints weight = 111982.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.041719 restraints weight = 88689.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.042008 restraints weight = 73575.121| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17802 Z= 0.128 Angle : 0.542 7.826 24081 Z= 0.293 Chirality : 0.041 0.186 2651 Planarity : 0.003 0.037 2973 Dihedral : 13.241 175.991 2654 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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: 0.11 (0.19), residues: 2022 helix: 1.27 (0.17), residues: 901 sheet: 0.19 (0.28), residues: 371 loop : -1.47 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 110 TYR 0.018 0.001 TYR H 184 PHE 0.027 0.002 PHE K 85 TRP 0.016 0.001 TRP F 339 HIS 0.003 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (17801) covalent geometry : angle 0.54178 / 0.29 (24079) SS BOND : bond 0.00418 / 0.22 ( 1) SS BOND : angle 1.70002 / 0.94 ( 2) hydrogen bonds : bond 0.03625 / 2.52 ( 800) hydrogen bonds : angle 4.91068 / 3.36 ( 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 142 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 ASP cc_start: 0.9494 (t0) cc_final: 0.9082 (m-30) REVERT: C 55 MET cc_start: 0.9472 (tpt) cc_final: 0.9189 (tpt) REVERT: E 24 MET cc_start: 0.7692 (ttt) cc_final: 0.6177 (ppp) REVERT: E 49 PHE cc_start: 0.9788 (t80) cc_final: 0.9478 (t80) REVERT: E 51 LYS cc_start: 0.9128 (mmpt) cc_final: 0.8896 (mmmt) REVERT: E 56 LEU cc_start: 0.8977 (tp) cc_final: 0.8624 (tp) REVERT: E 116 LEU cc_start: 0.9678 (tp) cc_final: 0.8967 (tp) REVERT: E 119 MET cc_start: 0.8789 (mmt) cc_final: 0.8084 (mmm) REVERT: F 8 MET cc_start: 0.9746 (mmp) cc_final: 0.9531 (mmm) REVERT: F 189 TRP cc_start: 0.9252 (m-10) cc_final: 0.9003 (m-10) REVERT: F 363 MET cc_start: 0.9223 (mmm) cc_final: 0.8602 (mmm) REVERT: F 420 ASP cc_start: 0.9643 (m-30) cc_final: 0.9121 (t0) REVERT: F 589 PHE cc_start: 0.9612 (t80) cc_final: 0.9349 (t80) REVERT: F 624 MET cc_start: 0.7851 (mmm) cc_final: 0.7286 (mpp) REVERT: H 28 MET cc_start: 0.9621 (mtp) cc_final: 0.9398 (ttt) REVERT: H 226 MET cc_start: 0.8663 (mmm) cc_final: 0.8416 (mmm) REVERT: I 86 TYR cc_start: 0.8822 (m-80) cc_final: 0.8319 (m-80) REVERT: I 120 PHE cc_start: 0.9556 (t80) cc_final: 0.9190 (t80) REVERT: K 45 THR cc_start: 0.8938 (p) cc_final: 0.8130 (p) REVERT: K 52 MET cc_start: 0.9830 (ptp) cc_final: 0.9399 (tpt) REVERT: K 83 ILE cc_start: 0.9594 (mm) cc_final: 0.9156 (mm) REVERT: K 86 TYR cc_start: 0.9688 (m-10) cc_final: 0.9417 (m-80) REVERT: K 126 TYR cc_start: 0.9295 (m-10) cc_final: 0.8987 (m-80) REVERT: K 127 PHE cc_start: 0.9808 (t80) cc_final: 0.9037 (t80) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.1340 time to fit residues: 29.3888 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 : 0.779 ------------------------------------------------------------------------------- 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: 0.7980 chunk 177 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H 129 GLN ** H 214 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 = 0.3173 r_free = 0.3173 target = 0.046575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.039388 restraints weight = 259028.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040236 restraints weight = 161387.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.040780 restraints weight = 112803.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.041171 restraints weight = 87769.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.041422 restraints weight = 73057.849| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17802 Z= 0.136 Angle : 0.553 8.619 24081 Z= 0.299 Chirality : 0.041 0.319 2651 Planarity : 0.003 0.042 2973 Dihedral : 13.176 176.097 2654 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: 0.09 (0.19), residues: 2022 helix: 1.22 (0.17), residues: 900 sheet: 0.20 (0.28), residues: 371 loop : -1.44 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 110 TYR 0.024 0.001 TYR E 57 PHE 0.034 0.002 PHE E 62 TRP 0.017 0.001 TRP F 339 HIS 0.005 0.001 HIS H 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (17801) covalent geometry : angle 0.55274 / 0.30 (24079) SS BOND : bond 0.00389 / 0.20 ( 1) SS BOND : angle 1.52216 / 0.84 ( 2) hydrogen bonds : bond 0.03557 / 2.46 ( 800) hydrogen bonds : angle 4.91769 / 3.37 ( 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 141 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.651 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: 0.9611 (mmp) cc_final: 0.9385 (mmm) REVERT: B 115 ASP cc_start: 0.9599 (t0) cc_final: 0.9346 (m-30) REVERT: C 55 MET cc_start: 0.9488 (tpt) cc_final: 0.9159 (tpt) REVERT: E 24 MET cc_start: 0.7652 (ttt) cc_final: 0.6175 (ppp) REVERT: E 49 PHE cc_start: 0.9759 (t80) cc_final: 0.9410 (t80) REVERT: E 51 LYS cc_start: 0.9141 (mmpt) cc_final: 0.8898 (mmmt) REVERT: E 56 LEU cc_start: 0.8801 (tp) cc_final: 0.8468 (tp) REVERT: E 116 LEU cc_start: 0.9641 (tp) cc_final: 0.8970 (tp) REVERT: E 119 MET cc_start: 0.8693 (mmt) cc_final: 0.7758 (mmp) REVERT: F 8 MET cc_start: 0.9741 (mmp) cc_final: 0.9535 (mmm) REVERT: F 363 MET cc_start: 0.9259 (mmm) cc_final: 0.8654 (mmm) REVERT: F 420 ASP cc_start: 0.9651 (m-30) cc_final: 0.9141 (t0) REVERT: F 589 PHE cc_start: 0.9621 (t80) cc_final: 0.9362 (t80) REVERT: F 624 MET cc_start: 0.7860 (mmm) cc_final: 0.7433 (mpp) REVERT: H 28 MET cc_start: 0.9643 (mtp) cc_final: 0.9414 (ttt) REVERT: H 129 GLN cc_start: 0.9683 (mm110) cc_final: 0.9385 (mp10) REVERT: H 226 MET cc_start: 0.8663 (mmm) cc_final: 0.8397 (mmm) REVERT: I 85 PHE cc_start: 0.9778 (m-10) cc_final: 0.9542 (m-10) REVERT: I 86 TYR cc_start: 0.8892 (m-80) cc_final: 0.8636 (m-80) REVERT: I 120 PHE cc_start: 0.9658 (t80) cc_final: 0.9332 (t80) REVERT: K 45 THR cc_start: 0.8983 (p) cc_final: 0.8259 (p) REVERT: K 52 MET cc_start: 0.9810 (ptp) cc_final: 0.9352 (tpt) REVERT: K 83 ILE cc_start: 0.9536 (mm) cc_final: 0.9099 (mm) REVERT: K 86 TYR cc_start: 0.9709 (m-10) cc_final: 0.9445 (m-80) REVERT: K 123 TYR cc_start: 0.9846 (t80) cc_final: 0.9525 (t80) REVERT: K 127 PHE cc_start: 0.9810 (t80) cc_final: 0.9007 (t80) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1320 time to fit residues: 28.8677 Evaluate side-chains 109 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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: 0.8980 chunk 158 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN C 72 HIS ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN C 168 ASN E 317 GLN ** 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 314 HIS F 334 ASN F 689 HIS ** H 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.041551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.034675 restraints weight = 281680.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.035371 restraints weight = 176572.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.035799 restraints weight = 126056.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.036145 restraints weight = 100562.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.036401 restraints weight = 84532.224| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 17802 Z= 0.304 Angle : 0.802 9.169 24081 Z= 0.437 Chirality : 0.046 0.334 2651 Planarity : 0.005 0.073 2973 Dihedral : 13.430 177.430 2654 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 25.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.17), residues: 2022 helix: 0.23 (0.16), residues: 915 sheet: -0.27 (0.27), residues: 376 loop : -1.76 (0.20), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 110 TYR 0.042 0.003 TYR K 136 PHE 0.028 0.003 PHE C 152 TRP 0.056 0.004 TRP H 52 HIS 0.014 0.003 HIS H 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.30 (17801) covalent geometry : angle 0.80207 / 0.44 (24079) SS BOND : bond 0.01134 / 0.60 ( 1) SS BOND : angle 1.89120 / 1.03 ( 2) hydrogen bonds : bond 0.04672 / 3.23 ( 800) hydrogen bonds : angle 5.49689 / 3.76 ( 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 132 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.656 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: C 55 MET cc_start: 0.9430 (tpt) cc_final: 0.9192 (tpt) REVERT: E 24 MET cc_start: 0.8071 (ttt) cc_final: 0.7492 (ppp) REVERT: E 49 PHE cc_start: 0.9618 (t80) cc_final: 0.9322 (t80) REVERT: E 51 LYS cc_start: 0.9244 (mmpt) cc_final: 0.8983 (mmmt) REVERT: E 119 MET cc_start: 0.8584 (mmt) cc_final: 0.7958 (mmm) REVERT: F 47 PHE cc_start: 0.8665 (m-80) cc_final: 0.8128 (m-80) REVERT: F 363 MET cc_start: 0.9423 (mmm) cc_final: 0.8900 (mmm) REVERT: F 420 ASP cc_start: 0.9626 (m-30) cc_final: 0.9174 (t0) REVERT: F 496 MET cc_start: 0.7808 (ppp) cc_final: 0.7401 (pmm) REVERT: F 589 PHE cc_start: 0.9649 (t80) cc_final: 0.9423 (t80) REVERT: F 624 MET cc_start: 0.8024 (mmm) cc_final: 0.7744 (mpp) REVERT: H 28 MET cc_start: 0.9720 (mtp) cc_final: 0.9315 (ttt) REVERT: I 49 ARG cc_start: 0.9028 (mtm180) cc_final: 0.8561 (ptt180) REVERT: I 120 PHE cc_start: 0.9634 (t80) cc_final: 0.9365 (t80) REVERT: K 45 THR cc_start: 0.9590 (p) cc_final: 0.9223 (p) REVERT: K 52 MET cc_start: 0.9815 (ptp) cc_final: 0.9398 (tpt) REVERT: K 109 ASP cc_start: 0.9521 (t70) cc_final: 0.9151 (m-30) REVERT: K 123 TYR cc_start: 0.9836 (t80) cc_final: 0.9535 (t80) REVERT: K 127 PHE cc_start: 0.9830 (t80) cc_final: 0.9117 (t80) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1473 time to fit residues: 29.3848 Evaluate side-chains 101 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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: 1.9990 chunk 109 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 82 optimal weight: 0.0570 chunk 76 optimal weight: 9.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 689 HIS H 177 ASN ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.043512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.036548 restraints weight = 270780.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.037317 restraints weight = 167065.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.037872 restraints weight = 118222.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.038235 restraints weight = 90614.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.038437 restraints weight = 74720.009| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17802 Z= 0.144 Angle : 0.596 9.394 24081 Z= 0.323 Chirality : 0.042 0.272 2651 Planarity : 0.004 0.074 2973 Dihedral : 13.311 176.217 2654 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2022 helix: 0.71 (0.17), residues: 909 sheet: -0.12 (0.28), residues: 362 loop : -1.54 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 52 TYR 0.023 0.002 TYR I 86 PHE 0.028 0.002 PHE K 85 TRP 0.016 0.002 TRP F 339 HIS 0.005 0.001 HIS H 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (17801) covalent geometry : angle 0.59578 / 0.32 (24079) SS BOND : bond 0.00321 / 0.17 ( 1) SS BOND : angle 2.22127 / 1.21 ( 2) hydrogen bonds : bond 0.03727 / 2.57 ( 800) hydrogen bonds : angle 5.14974 / 3.54 ( 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 132 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.686 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: 0.9601 (mmp) cc_final: 0.9400 (mmm) REVERT: C 55 MET cc_start: 0.9453 (tpt) cc_final: 0.9188 (tpt) REVERT: E 24 MET cc_start: 0.7908 (ttt) cc_final: 0.7237 (ppp) REVERT: E 56 LEU cc_start: 0.8892 (tp) cc_final: 0.8682 (tp) REVERT: E 119 MET cc_start: 0.8334 (mmt) cc_final: 0.7379 (mmm) REVERT: F 47 PHE cc_start: 0.8652 (m-80) cc_final: 0.8041 (m-80) REVERT: F 189 TRP cc_start: 0.9614 (m-10) cc_final: 0.9119 (m-10) REVERT: F 363 MET cc_start: 0.9330 (mmm) cc_final: 0.8814 (mmm) REVERT: F 420 ASP cc_start: 0.9617 (m-30) cc_final: 0.9153 (t0) REVERT: F 452 MET cc_start: 0.8924 (mmp) cc_final: 0.8713 (mmm) REVERT: F 496 MET cc_start: 0.8294 (ppp) cc_final: 0.7411 (pmm) REVERT: F 589 PHE cc_start: 0.9641 (t80) cc_final: 0.9429 (t80) REVERT: F 624 MET cc_start: 0.7988 (mmm) cc_final: 0.7646 (mpp) REVERT: H 28 MET cc_start: 0.9622 (mtp) cc_final: 0.9276 (ttt) REVERT: I 49 ARG cc_start: 0.9127 (mtm180) cc_final: 0.8840 (ptt180) REVERT: I 54 GLN cc_start: 0.9244 (mp10) cc_final: 0.8848 (mp10) REVERT: I 85 PHE cc_start: 0.9819 (m-10) cc_final: 0.9600 (m-10) REVERT: I 120 PHE cc_start: 0.9574 (t80) cc_final: 0.9357 (t80) REVERT: K 45 THR cc_start: 0.9517 (p) cc_final: 0.9137 (p) REVERT: K 52 MET cc_start: 0.9808 (ptp) cc_final: 0.9398 (tpt) REVERT: K 54 GLN cc_start: 0.9739 (tp-100) cc_final: 0.9525 (tp-100) REVERT: K 83 ILE cc_start: 0.9518 (mm) cc_final: 0.9168 (mm) REVERT: K 86 TYR cc_start: 0.9686 (m-10) cc_final: 0.9424 (m-80) REVERT: K 123 TYR cc_start: 0.9808 (t80) cc_final: 0.9511 (t80) REVERT: K 127 PHE cc_start: 0.9808 (t80) cc_final: 0.8990 (t80) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1394 time to fit residues: 27.8856 Evaluate side-chains 105 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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: 5.9990 chunk 134 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 689 HIS ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.043546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.036564 restraints weight = 270122.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037340 restraints weight = 167863.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.037873 restraints weight = 118227.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.038213 restraints weight = 90754.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.038457 restraints weight = 75587.432| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17802 Z= 0.137 Angle : 0.576 7.926 24081 Z= 0.313 Chirality : 0.042 0.265 2651 Planarity : 0.003 0.067 2973 Dihedral : 13.210 175.827 2654 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % 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: -0.33 (0.18), residues: 2022 helix: 0.84 (0.17), residues: 907 sheet: -0.17 (0.28), residues: 371 loop : -1.52 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 110 TYR 0.020 0.002 TYR I 86 PHE 0.020 0.002 PHE E 62 TRP 0.015 0.001 TRP F 339 HIS 0.005 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (17801) covalent geometry : angle 0.57632 / 0.31 (24079) SS BOND : bond 0.00482 / 0.25 ( 1) SS BOND : angle 1.43557 / 0.80 ( 2) hydrogen bonds : bond 0.03647 / 2.53 ( 800) hydrogen bonds : angle 5.08055 / 3.50 ( 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 128 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.466 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: C 55 MET cc_start: 0.9463 (tpt) cc_final: 0.9197 (tpt) REVERT: E 24 MET cc_start: 0.7903 (ttt) cc_final: 0.6925 (ppp) REVERT: E 40 MET cc_start: 0.9406 (mmp) cc_final: 0.8787 (tmm) REVERT: E 51 LYS cc_start: 0.9141 (mmpt) cc_final: 0.8895 (mmmt) REVERT: E 56 LEU cc_start: 0.9023 (tp) cc_final: 0.8796 (tp) REVERT: E 119 MET cc_start: 0.8341 (mmt) cc_final: 0.7438 (mmm) REVERT: F 1 MET cc_start: 0.7961 (tpt) cc_final: 0.7639 (tmm) REVERT: F 8 MET cc_start: 0.9740 (mmp) cc_final: 0.9531 (mmm) REVERT: F 47 PHE cc_start: 0.8609 (m-80) cc_final: 0.7920 (m-80) REVERT: F 189 TRP cc_start: 0.9609 (m-10) cc_final: 0.9146 (m-10) REVERT: F 363 MET cc_start: 0.9358 (mmm) cc_final: 0.8869 (mmm) REVERT: F 420 ASP cc_start: 0.9645 (m-30) cc_final: 0.9259 (t0) REVERT: F 452 MET cc_start: 0.8951 (mmp) cc_final: 0.8741 (mmm) REVERT: F 496 MET cc_start: 0.7949 (ppp) cc_final: 0.7302 (pmm) REVERT: F 624 MET cc_start: 0.8001 (mmm) cc_final: 0.7622 (mpp) REVERT: H 28 MET cc_start: 0.9640 (mtp) cc_final: 0.9298 (ttt) REVERT: H 184 TYR cc_start: 0.9406 (m-80) cc_final: 0.9018 (m-80) REVERT: H 226 MET cc_start: 0.8739 (mmm) cc_final: 0.8480 (mmm) REVERT: I 49 ARG cc_start: 0.9267 (mtm180) cc_final: 0.8829 (ptt180) REVERT: I 85 PHE cc_start: 0.9827 (m-10) cc_final: 0.9572 (m-10) REVERT: I 120 PHE cc_start: 0.9571 (t80) cc_final: 0.9344 (t80) REVERT: K 45 THR cc_start: 0.9530 (p) cc_final: 0.9160 (p) REVERT: K 52 MET cc_start: 0.9797 (ptp) cc_final: 0.9295 (tpt) REVERT: K 83 ILE cc_start: 0.9522 (mm) cc_final: 0.9135 (mm) REVERT: K 86 TYR cc_start: 0.9682 (m-10) cc_final: 0.9418 (m-80) REVERT: K 123 TYR cc_start: 0.9807 (t80) cc_final: 0.9488 (t80) REVERT: K 127 PHE cc_start: 0.9828 (t80) cc_final: 0.8976 (t80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1454 time to fit residues: 28.3934 Evaluate side-chains 103 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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: 3.9990 chunk 188 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 20 optimal weight: 10.9990 chunk 88 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.043714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036696 restraints weight = 270002.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.037474 restraints weight = 167581.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.037984 restraints weight = 116992.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.038364 restraints weight = 90879.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.038610 restraints weight = 74398.374| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17802 Z= 0.128 Angle : 0.563 7.639 24081 Z= 0.305 Chirality : 0.041 0.257 2651 Planarity : 0.003 0.058 2973 Dihedral : 13.131 175.803 2654 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.18), residues: 2022 helix: 0.94 (0.17), residues: 913 sheet: -0.19 (0.28), residues: 371 loop : -1.49 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 110 TYR 0.035 0.002 TYR I 86 PHE 0.036 0.002 PHE E 49 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 0.00262 / 0.13 (17801) covalent geometry : angle 0.56241 / 0.31 (24079) SS BOND : bond 0.00442 / 0.23 ( 1) SS BOND : angle 1.39506 / 0.77 ( 2) hydrogen bonds : bond 0.03620 / 2.51 ( 800) hydrogen bonds : angle 4.98345 / 3.44 ( 2325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2390.88 seconds wall clock time: 42 minutes 47.06 seconds (2567.06 seconds total)