Starting phenix.real_space_refine on Thu Jul 2 16:22:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25nx_80238/07_2026/25nx_80238_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/25nx_80238/07_2026/25nx_80238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/25nx_80238/07_2026/25nx_80238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25nx_80238/07_2026/25nx_80238.map" model { file = "/net/cci-nas-00/data/ceres_data/25nx_80238/07_2026/25nx_80238_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25nx_80238/07_2026/25nx_80238_neut.cif" } resolution = 2.86 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= -0.000 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5743 2.51 5 N 1583 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s 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: 9040 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1942 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2569 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 425 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 268 Unusual residues: {'XCP': 3} Classifications: {'peptide': 29, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'XCP:plan-1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2883 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 357} Chain breaks: 2 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 7, 'ASP:plan': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 90 Time building chain proxies: 1.59, per 1000 atoms: 0.18 Number of scatterers: 9040 At special positions: 0 Unit cell: (73.1, 98.04, 173.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1656 8.00 N 1583 7.00 C 5743 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " 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: 1.78 Conformation dependent library (CDL) restraints added in 448.1 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB XCP P 24 " pdb=" CB XCP P 28 " pdb=" CB XCP P 31 " Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 42.1% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.907A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.585A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.676A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.566A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.587A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 53 removed outlier: 3.500A pdb=" N ARG R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 172 Processing helix chain 'R' and resid 178 through 212 removed outlier: 3.645A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.699A pdb=" N ARG R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.640A pdb=" N TYR R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.572A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 391 removed outlier: 3.859A pdb=" N GLN R 364 " --> pdb=" O LYS R 360 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 365 " --> pdb=" O TRP R 361 " (cutoff:3.500A) Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 398 through 413 Processing helix chain 'R' and resid 413 through 418 Processing helix chain 'R' and resid 419 through 423 removed outlier: 3.600A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 460 removed outlier: 3.580A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 479 removed outlier: 3.659A pdb=" N LEU R 479 " --> pdb=" O SER R 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 4.382A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.541A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.599A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.724A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.603A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.873A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.549A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.793A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.610A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 Processing sheet with id=AB3, first strand: chain 'R' and resid 125 through 130 474 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.73 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: 2939 1.34 - 1.46: 1675 1.46 - 1.58: 4550 1.58 - 1.70: 0 1.70 - 1.81: 81 Bond restraints: 9245 Sorted by residual: bond pdb=" N ILE R 237 " pdb=" CA ILE R 237 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.28e+00 bond pdb=" N ILE R 190 " pdb=" CA ILE R 190 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" N VAL B 100 " pdb=" CA VAL B 100 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.46e+00 bond pdb=" N ILE P 15 " pdb=" CA ILE P 15 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.14e-02 7.69e+03 8.31e+00 bond pdb=" N LEU R 292 " pdb=" CA LEU R 292 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.28e-02 6.10e+03 8.25e+00 ... (remaining 9240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 12021 1.60 - 3.19: 450 3.19 - 4.79: 67 4.79 - 6.38: 6 6.38 - 7.98: 2 Bond angle restraints: 12546 Sorted by residual: angle pdb=" N GLU G 17 " pdb=" CA GLU G 17 " pdb=" CB GLU G 17 " ideal model delta sigma weight residual 110.16 116.13 -5.97 1.48e+00 4.57e-01 1.63e+01 angle pdb=" N MET B 101 " pdb=" CA MET B 101 " pdb=" C MET B 101 " ideal model delta sigma weight residual 114.39 108.88 5.51 1.45e+00 4.76e-01 1.44e+01 angle pdb=" N TYR R 195 " pdb=" CA TYR R 195 " pdb=" C TYR R 195 " ideal model delta sigma weight residual 112.54 108.12 4.42 1.22e+00 6.72e-01 1.31e+01 angle pdb=" CA TYR R 191 " pdb=" CB TYR R 191 " pdb=" CG TYR R 191 " ideal model delta sigma weight residual 113.90 120.33 -6.43 1.80e+00 3.09e-01 1.27e+01 angle pdb=" CB ARG R 43 " pdb=" CG ARG R 43 " pdb=" CD ARG R 43 " ideal model delta sigma weight residual 111.30 119.28 -7.98 2.30e+00 1.89e-01 1.20e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5056 17.87 - 35.74: 315 35.74 - 53.61: 49 53.61 - 71.48: 10 71.48 - 89.35: 9 Dihedral angle restraints: 5439 sinusoidal: 2080 harmonic: 3359 Sorted by residual: dihedral pdb=" CA LEU P 27 " pdb=" C LEU P 27 " pdb=" N XCP P 28 " pdb=" CA XCP P 28 " ideal model delta harmonic sigma weight residual 180.00 139.70 40.30 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA GLU P 30 " pdb=" C GLU P 30 " pdb=" N XCP P 31 " pdb=" CA XCP P 31 " ideal model delta harmonic sigma weight residual 180.00 140.41 39.59 0 5.00e+00 4.00e-02 6.27e+01 dihedral pdb=" CA PHE P 23 " pdb=" C PHE P 23 " pdb=" N XCP P 24 " pdb=" CA XCP P 24 " ideal model delta harmonic sigma weight residual 180.00 140.77 39.23 0 5.00e+00 4.00e-02 6.16e+01 ... (remaining 5436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 882 0.037 - 0.074: 364 0.074 - 0.111: 103 0.111 - 0.148: 35 0.148 - 0.185: 10 Chirality restraints: 1394 Sorted by residual: chirality pdb=" CA LEU P 18 " pdb=" N LEU P 18 " pdb=" C LEU P 18 " pdb=" CB LEU P 18 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA ILE P 15 " pdb=" N ILE P 15 " pdb=" C ILE P 15 " pdb=" CB ILE P 15 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA TYR R 191 " pdb=" N TYR R 191 " pdb=" C TYR R 191 " pdb=" CB TYR R 191 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 1391 not shown) Planarity restraints: 1607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 325 " -0.051 5.00e-02 4.00e+02 7.70e-02 9.49e+00 pdb=" N PRO A 326 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 366 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.63e+00 pdb=" C PRO R 366 " 0.033 2.00e-02 2.50e+03 pdb=" O PRO R 366 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE R 367 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 191 " 0.012 2.00e-02 2.50e+03 1.12e-02 2.50e+00 pdb=" CG TYR R 191 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR R 191 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR R 191 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR R 191 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 191 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR R 191 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR R 191 " 0.001 2.00e-02 2.50e+03 ... (remaining 1604 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 310 2.70 - 3.25: 9273 3.25 - 3.80: 15016 3.80 - 4.35: 18939 4.35 - 4.90: 32368 Nonbonded interactions: 75906 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.154 3.040 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.203 3.040 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.245 3.120 nonbonded pdb=" O LEU R 215 " pdb=" ND2 ASN R 220 " model vdw 2.259 3.120 nonbonded pdb=" OH TYR A 360 " pdb=" OD2 ASP A 381 " model vdw 2.262 3.040 ... (remaining 75901 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.640 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 : 0.005 0.041 9251 Z= 0.296 Angle : 0.693 7.976 12558 Z= 0.449 Chirality : 0.046 0.185 1394 Planarity : 0.004 0.077 1607 Dihedral : 12.331 89.354 3253 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.43 % Allowed : 0.54 % Favored : 99.04 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 0.52 (0.26), residues: 1130 helix: 1.10 (0.26), residues: 443 sheet: -0.02 (0.33), residues: 238 loop : -0.07 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 43 TYR 0.027 0.002 TYR R 191 PHE 0.014 0.001 PHE R 315 TRP 0.010 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.30 ( 9245) covalent geometry : angle 0.69308 / 0.45 (12546) SS BOND : bond 0.00144 / 0.08 ( 6) SS BOND : angle 0.90571 / 0.71 ( 12) hydrogen bonds : bond 0.17435 / 11.89 ( 474) hydrogen bonds : angle 6.82870 / 4.93 ( 1350) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 GLU cc_start: 0.8364 (tp30) cc_final: 0.7824 (tp30) REVERT: B 78 LYS cc_start: 0.8209 (mmtm) cc_final: 0.7913 (mmtp) REVERT: N 73 ASP cc_start: 0.8145 (t70) cc_final: 0.7894 (t70) REVERT: R 32 MET cc_start: 0.6983 (tpt) cc_final: 0.6576 (tpt) REVERT: R 185 ASP cc_start: 0.8144 (m-30) cc_final: 0.7800 (m-30) outliers start: 4 outliers final: 0 residues processed: 182 average time/residue: 0.7183 time to fit residues: 137.8324 Evaluate side-chains 136 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS P 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.085175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.060639 restraints weight = 22217.621| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.12 r_work: 0.2738 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9251 Z= 0.176 Angle : 0.600 8.836 12558 Z= 0.317 Chirality : 0.043 0.143 1394 Planarity : 0.004 0.047 1607 Dihedral : 4.394 25.220 1269 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.28 % Allowed : 11.13 % Favored : 87.58 % Cbeta Deviations : 0.28 % 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: 1.02 (0.26), residues: 1130 helix: 1.90 (0.26), residues: 443 sheet: -0.07 (0.33), residues: 229 loop : -0.04 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 20 TYR 0.034 0.001 TYR R 191 PHE 0.017 0.001 PHE R 315 TRP 0.015 0.001 TRP B 169 HIS 0.020 0.001 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 9245) covalent geometry : angle 0.59976 / 0.32 (12546) SS BOND : bond 0.00155 / 0.08 ( 6) SS BOND : angle 0.89350 / 0.54 ( 12) hydrogen bonds : bond 0.05030 / 3.34 ( 474) hydrogen bonds : angle 4.69918 / 3.41 ( 1350) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 GLU cc_start: 0.9055 (tp30) cc_final: 0.8407 (tp30) REVERT: B 59 TYR cc_start: 0.9443 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: B 215 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7613 (pp20) REVERT: B 254 ASP cc_start: 0.8437 (t70) cc_final: 0.8148 (t0) REVERT: B 312 ASP cc_start: 0.8922 (m-30) cc_final: 0.8506 (m-30) REVERT: G 46 LYS cc_start: 0.9465 (mtmm) cc_final: 0.9261 (mppt) REVERT: N 43 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8341 (mtpt) REVERT: N 73 ASP cc_start: 0.8519 (t70) cc_final: 0.8109 (t0) REVERT: N 120 GLN cc_start: 0.8917 (tp-100) cc_final: 0.8666 (tp-100) REVERT: R 32 MET cc_start: 0.8414 (tpt) cc_final: 0.7608 (pmm) REVERT: R 136 TYR cc_start: 0.8946 (t80) cc_final: 0.8741 (t80) REVERT: R 185 ASP cc_start: 0.8971 (m-30) cc_final: 0.8490 (m-30) REVERT: R 315 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7432 (t80) outliers start: 12 outliers final: 4 residues processed: 152 average time/residue: 0.7080 time to fit residues: 113.6780 Evaluate side-chains 140 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 315 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 101 optimal weight: 0.3980 chunk 84 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN N 123 GLN R 307 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.086850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.062650 restraints weight = 21994.366| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.10 r_work: 0.2775 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9251 Z= 0.117 Angle : 0.555 8.451 12558 Z= 0.291 Chirality : 0.041 0.149 1394 Planarity : 0.004 0.041 1607 Dihedral : 4.237 22.500 1269 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.28 % Allowed : 14.13 % Favored : 84.58 % Cbeta Deviations : 0.28 % 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: 1.14 (0.26), residues: 1130 helix: 2.06 (0.26), residues: 443 sheet: 0.14 (0.35), residues: 216 loop : -0.13 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 13 TYR 0.028 0.001 TYR R 191 PHE 0.016 0.001 PHE R 315 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9245) covalent geometry : angle 0.55481 / 0.29 (12546) SS BOND : bond 0.00102 / 0.05 ( 6) SS BOND : angle 0.71671 / 0.42 ( 12) hydrogen bonds : bond 0.04289 / 2.84 ( 474) hydrogen bonds : angle 4.37016 / 3.16 ( 1350) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.7794 (mtm110) REVERT: A 393 LEU cc_start: 0.9500 (mt) cc_final: 0.9299 (mp) REVERT: B 12 GLU cc_start: 0.9021 (tp30) cc_final: 0.8335 (tp30) REVERT: B 215 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7590 (pp20) REVERT: B 254 ASP cc_start: 0.8409 (t70) cc_final: 0.8122 (t0) REVERT: B 312 ASP cc_start: 0.8697 (m-30) cc_final: 0.8442 (m-30) REVERT: G 46 LYS cc_start: 0.9444 (mtmm) cc_final: 0.9235 (mppt) REVERT: N 3 GLN cc_start: 0.8581 (mm-40) cc_final: 0.7996 (tp40) REVERT: N 46 GLU cc_start: 0.8877 (tt0) cc_final: 0.8552 (tt0) REVERT: R 185 ASP cc_start: 0.8953 (m-30) cc_final: 0.8459 (m-30) REVERT: R 214 ARG cc_start: 0.8841 (ttm170) cc_final: 0.8636 (ttm-80) outliers start: 12 outliers final: 4 residues processed: 154 average time/residue: 0.7132 time to fit residues: 116.0440 Evaluate side-chains 141 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 42 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 4 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 104 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 120 GLN ** R 307 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 = 0.3446 r_free = 0.3446 target = 0.087662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.063419 restraints weight = 22104.356| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.13 r_work: 0.2800 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9251 Z= 0.105 Angle : 0.522 6.462 12558 Z= 0.277 Chirality : 0.040 0.137 1394 Planarity : 0.004 0.049 1607 Dihedral : 4.117 21.939 1269 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.82 % Allowed : 15.10 % Favored : 83.08 % Cbeta Deviations : 0.28 % 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: 1.25 (0.26), residues: 1130 helix: 2.15 (0.26), residues: 443 sheet: 0.35 (0.35), residues: 220 loop : -0.16 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 13 TYR 0.025 0.001 TYR R 191 PHE 0.014 0.001 PHE R 315 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 9245) covalent geometry : angle 0.52223 / 0.28 (12546) SS BOND : bond 0.00088 / 0.05 ( 6) SS BOND : angle 0.67282 / 0.39 ( 12) hydrogen bonds : bond 0.03882 / 2.54 ( 474) hydrogen bonds : angle 4.16212 / 2.98 ( 1350) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8691 (tp30) REVERT: A 33 ASP cc_start: 0.9253 (m-30) cc_final: 0.8721 (m-30) REVERT: A 393 LEU cc_start: 0.9493 (mt) cc_final: 0.9282 (mp) REVERT: B 10 GLU cc_start: 0.9018 (pp20) cc_final: 0.8636 (pp20) REVERT: B 12 GLU cc_start: 0.8985 (tp30) cc_final: 0.8289 (tp30) REVERT: B 215 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7591 (pp20) REVERT: B 254 ASP cc_start: 0.8385 (t70) cc_final: 0.8126 (t0) REVERT: B 312 ASP cc_start: 0.8667 (m-30) cc_final: 0.8364 (m-30) REVERT: G 16 VAL cc_start: 0.8898 (t) cc_final: 0.8664 (t) REVERT: G 46 LYS cc_start: 0.9434 (mtmm) cc_final: 0.9191 (mppt) REVERT: G 58 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8496 (pm20) REVERT: N 3 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8197 (tp40) REVERT: N 43 LYS cc_start: 0.8418 (mtpt) cc_final: 0.8158 (mtpp) REVERT: N 46 GLU cc_start: 0.8825 (tt0) cc_final: 0.8475 (tt0) REVERT: N 73 ASP cc_start: 0.8513 (t0) cc_final: 0.8068 (t70) REVERT: N 76 LYS cc_start: 0.9617 (mtpp) cc_final: 0.9225 (ptpp) REVERT: R 185 ASP cc_start: 0.8950 (m-30) cc_final: 0.8457 (m-30) REVERT: R 469 GLU cc_start: 0.8957 (tp30) cc_final: 0.8456 (tm-30) outliers start: 17 outliers final: 5 residues processed: 157 average time/residue: 0.6633 time to fit residues: 110.4541 Evaluate side-chains 145 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 224 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 307 HIS R 393 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.086445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.061803 restraints weight = 21976.744| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.16 r_work: 0.2767 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9251 Z= 0.140 Angle : 0.543 10.728 12558 Z= 0.285 Chirality : 0.041 0.136 1394 Planarity : 0.004 0.042 1607 Dihedral : 4.109 24.168 1269 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.71 % Allowed : 16.81 % Favored : 81.48 % Cbeta Deviations : 0.28 % 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: 1.25 (0.26), residues: 1130 helix: 2.10 (0.25), residues: 447 sheet: 0.36 (0.35), residues: 220 loop : -0.13 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 13 TYR 0.023 0.001 TYR R 191 PHE 0.014 0.001 PHE R 315 TRP 0.011 0.001 TRP B 169 HIS 0.019 0.001 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9245) covalent geometry : angle 0.54293 / 0.28 (12546) SS BOND : bond 0.00136 / 0.07 ( 6) SS BOND : angle 0.65974 / 0.42 ( 12) hydrogen bonds : bond 0.04055 / 2.66 ( 474) hydrogen bonds : angle 4.17118 / 2.98 ( 1350) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.8295 (mtm-85) REVERT: A 27 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8710 (tp30) REVERT: A 31 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8516 (mm-40) REVERT: A 33 ASP cc_start: 0.9259 (m-30) cc_final: 0.8743 (m-30) REVERT: A 393 LEU cc_start: 0.9511 (mt) cc_final: 0.9291 (mp) REVERT: B 12 GLU cc_start: 0.8986 (tp30) cc_final: 0.8325 (tp30) REVERT: B 215 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7654 (pp20) REVERT: B 254 ASP cc_start: 0.8416 (t70) cc_final: 0.8141 (t0) REVERT: B 312 ASP cc_start: 0.8794 (m-30) cc_final: 0.8478 (m-30) REVERT: G 46 LYS cc_start: 0.9433 (mtmm) cc_final: 0.9205 (mppt) REVERT: N 3 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8151 (tp40) REVERT: N 43 LYS cc_start: 0.8551 (mtpt) cc_final: 0.8318 (mtpp) REVERT: N 46 GLU cc_start: 0.8860 (tt0) cc_final: 0.8436 (tt0) REVERT: N 73 ASP cc_start: 0.8519 (t0) cc_final: 0.8251 (t70) REVERT: N 76 LYS cc_start: 0.9571 (mtpp) cc_final: 0.9264 (mtmm) REVERT: R 180 GLU cc_start: 0.8558 (pm20) cc_final: 0.8197 (pm20) REVERT: R 185 ASP cc_start: 0.8939 (m-30) cc_final: 0.8472 (m-30) REVERT: R 469 GLU cc_start: 0.8922 (tp30) cc_final: 0.8681 (tm-30) outliers start: 16 outliers final: 7 residues processed: 148 average time/residue: 0.7195 time to fit residues: 112.3932 Evaluate side-chains 141 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain P residue 18 LEU Chi-restraints excluded: chain P residue 23 PHE Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 281 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 82 optimal weight: 30.0000 chunk 90 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 401 GLN ** 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 = 0.3431 r_free = 0.3431 target = 0.086941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.062455 restraints weight = 21894.410| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.13 r_work: 0.2781 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9251 Z= 0.122 Angle : 0.553 8.192 12558 Z= 0.292 Chirality : 0.040 0.145 1394 Planarity : 0.004 0.043 1607 Dihedral : 4.138 25.949 1269 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.82 % Allowed : 17.24 % Favored : 80.94 % Cbeta Deviations : 0.28 % 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: 1.26 (0.26), residues: 1130 helix: 2.10 (0.25), residues: 446 sheet: 0.40 (0.35), residues: 220 loop : -0.13 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 13 TYR 0.022 0.001 TYR R 191 PHE 0.014 0.001 PHE R 315 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9245) covalent geometry : angle 0.55331 / 0.29 (12546) SS BOND : bond 0.00125 / 0.06 ( 6) SS BOND : angle 0.62890 / 0.38 ( 12) hydrogen bonds : bond 0.03945 / 2.60 ( 474) hydrogen bonds : angle 4.15213 / 2.97 ( 1350) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8595 (mtm-85) cc_final: 0.8306 (mtm-85) REVERT: A 27 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8707 (tp30) REVERT: A 31 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8498 (mm-40) REVERT: A 33 ASP cc_start: 0.9262 (m-30) cc_final: 0.8734 (m-30) REVERT: A 60 MET cc_start: 0.8716 (mtt) cc_final: 0.8474 (mpt) REVERT: A 61 ARG cc_start: 0.8434 (mtt-85) cc_final: 0.8212 (tpp80) REVERT: A 393 LEU cc_start: 0.9516 (mt) cc_final: 0.9303 (mp) REVERT: B 10 GLU cc_start: 0.9067 (pp20) cc_final: 0.8749 (pp20) REVERT: B 12 GLU cc_start: 0.8968 (tp30) cc_final: 0.8268 (tp30) REVERT: B 134 ARG cc_start: 0.8458 (ptp-110) cc_final: 0.7836 (ptp90) REVERT: B 215 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7615 (pp20) REVERT: B 254 ASP cc_start: 0.8424 (t70) cc_final: 0.8156 (t0) REVERT: G 20 LYS cc_start: 0.9556 (mtmp) cc_final: 0.9317 (mtmm) REVERT: G 46 LYS cc_start: 0.9422 (mtmm) cc_final: 0.9199 (mppt) REVERT: N 3 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8194 (tp40) REVERT: N 43 LYS cc_start: 0.8433 (mtpt) cc_final: 0.8216 (mtpp) REVERT: N 46 GLU cc_start: 0.8857 (tt0) cc_final: 0.8379 (tt0) REVERT: N 73 ASP cc_start: 0.8483 (t0) cc_final: 0.8197 (t70) REVERT: N 76 LYS cc_start: 0.9564 (mtpp) cc_final: 0.9242 (mtmm) REVERT: P 21 ARG cc_start: 0.8343 (ppt170) cc_final: 0.8099 (ppt90) REVERT: R 180 GLU cc_start: 0.8538 (pm20) cc_final: 0.8168 (pm20) REVERT: R 185 ASP cc_start: 0.8936 (m-30) cc_final: 0.8492 (m-30) REVERT: R 469 GLU cc_start: 0.8868 (tp30) cc_final: 0.8623 (tm-30) outliers start: 17 outliers final: 4 residues processed: 156 average time/residue: 0.6864 time to fit residues: 113.3442 Evaluate side-chains 144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 281 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.085946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.061674 restraints weight = 22211.135| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.12 r_work: 0.2759 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9251 Z= 0.159 Angle : 0.584 11.966 12558 Z= 0.307 Chirality : 0.042 0.149 1394 Planarity : 0.004 0.048 1607 Dihedral : 4.231 27.381 1269 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.71 % Allowed : 18.31 % Favored : 79.98 % Cbeta Deviations : 0.28 % 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: 1.21 (0.25), residues: 1130 helix: 2.06 (0.25), residues: 446 sheet: 0.31 (0.35), residues: 222 loop : -0.11 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 13 TYR 0.022 0.001 TYR R 191 PHE 0.014 0.001 PHE R 315 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9245) covalent geometry : angle 0.58417 / 0.31 (12546) SS BOND : bond 0.00134 / 0.07 ( 6) SS BOND : angle 0.66785 / 0.41 ( 12) hydrogen bonds : bond 0.04173 / 2.74 ( 474) hydrogen bonds : angle 4.17836 / 2.99 ( 1350) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8605 (mtm-85) cc_final: 0.8308 (mtm-85) REVERT: A 27 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8714 (tp30) REVERT: A 31 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8520 (mm-40) REVERT: A 33 ASP cc_start: 0.9268 (m-30) cc_final: 0.8750 (m-30) REVERT: A 60 MET cc_start: 0.8716 (mtt) cc_final: 0.8500 (mpt) REVERT: A 393 LEU cc_start: 0.9511 (mt) cc_final: 0.9287 (mp) REVERT: B 12 GLU cc_start: 0.8975 (tp30) cc_final: 0.8310 (tp30) REVERT: B 134 ARG cc_start: 0.8439 (ptp-110) cc_final: 0.7934 (ptp90) REVERT: B 215 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7614 (pp20) REVERT: B 254 ASP cc_start: 0.8448 (t70) cc_final: 0.8171 (t0) REVERT: B 312 ASP cc_start: 0.8660 (m-30) cc_final: 0.8305 (t0) REVERT: G 46 LYS cc_start: 0.9423 (mtmm) cc_final: 0.9208 (mppt) REVERT: N 3 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8148 (tp40) REVERT: N 43 LYS cc_start: 0.8491 (mtpt) cc_final: 0.8170 (mtpt) REVERT: N 46 GLU cc_start: 0.8843 (tt0) cc_final: 0.8413 (tt0) REVERT: N 73 ASP cc_start: 0.8486 (t0) cc_final: 0.8188 (t70) REVERT: N 76 LYS cc_start: 0.9554 (mtpp) cc_final: 0.9223 (mtmm) REVERT: R 180 GLU cc_start: 0.8595 (pm20) cc_final: 0.8243 (pm20) REVERT: R 185 ASP cc_start: 0.8963 (m-30) cc_final: 0.8520 (m-30) REVERT: R 469 GLU cc_start: 0.8928 (tp30) cc_final: 0.8656 (tm-30) outliers start: 16 outliers final: 6 residues processed: 147 average time/residue: 0.7228 time to fit residues: 112.4599 Evaluate side-chains 143 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 281 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 123 GLN ** R 401 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 = 0.3416 r_free = 0.3416 target = 0.085463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.061304 restraints weight = 22128.852| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.07 r_work: 0.2753 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9251 Z= 0.164 Angle : 0.593 8.665 12558 Z= 0.314 Chirality : 0.042 0.145 1394 Planarity : 0.004 0.054 1607 Dihedral : 4.278 29.447 1269 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.61 % Allowed : 19.38 % Favored : 79.01 % Cbeta Deviations : 0.28 % 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: 1.16 (0.25), residues: 1130 helix: 2.01 (0.25), residues: 445 sheet: 0.31 (0.34), residues: 224 loop : -0.16 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 105 TYR 0.021 0.001 TYR R 191 PHE 0.015 0.001 PHE R 315 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 9245) covalent geometry : angle 0.59309 / 0.31 (12546) SS BOND : bond 0.00133 / 0.07 ( 6) SS BOND : angle 0.63747 / 0.39 ( 12) hydrogen bonds : bond 0.04146 / 2.71 ( 474) hydrogen bonds : angle 4.18693 / 2.99 ( 1350) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8597 (mtm-85) cc_final: 0.8303 (mtm-85) REVERT: A 27 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8734 (tp30) REVERT: A 31 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8515 (mm-40) REVERT: B 10 GLU cc_start: 0.9080 (pp20) cc_final: 0.8844 (pp20) REVERT: B 12 GLU cc_start: 0.8966 (tp30) cc_final: 0.8303 (tp30) REVERT: B 215 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7625 (pp20) REVERT: B 254 ASP cc_start: 0.8450 (t70) cc_final: 0.8140 (t0) REVERT: G 46 LYS cc_start: 0.9426 (mtmm) cc_final: 0.9214 (mppt) REVERT: N 3 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8129 (tp40) REVERT: N 46 GLU cc_start: 0.8814 (tt0) cc_final: 0.8399 (tt0) REVERT: N 73 ASP cc_start: 0.8480 (t0) cc_final: 0.8187 (t70) REVERT: N 76 LYS cc_start: 0.9543 (mtpp) cc_final: 0.9208 (mtmm) REVERT: R 180 GLU cc_start: 0.8590 (pm20) cc_final: 0.8247 (pm20) REVERT: R 185 ASP cc_start: 0.8936 (m-30) cc_final: 0.8490 (m-30) REVERT: R 469 GLU cc_start: 0.8954 (tp30) cc_final: 0.8652 (tm-30) outliers start: 15 outliers final: 6 residues processed: 148 average time/residue: 0.7125 time to fit residues: 111.4742 Evaluate side-chains 142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 281 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 402 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.084864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.060516 restraints weight = 22201.269| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.11 r_work: 0.2721 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9251 Z= 0.226 Angle : 0.672 13.440 12558 Z= 0.349 Chirality : 0.044 0.139 1394 Planarity : 0.004 0.060 1607 Dihedral : 4.424 30.972 1269 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.03 % Allowed : 19.38 % Favored : 78.59 % Cbeta Deviations : 0.28 % 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: 1.05 (0.25), residues: 1130 helix: 1.89 (0.25), residues: 445 sheet: 0.17 (0.34), residues: 232 loop : -0.13 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 105 TYR 0.021 0.001 TYR R 191 PHE 0.013 0.001 PHE R 315 TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 ( 9245) covalent geometry : angle 0.67202 / 0.35 (12546) SS BOND : bond 0.00241 / 0.12 ( 6) SS BOND : angle 0.71023 / 0.47 ( 12) hydrogen bonds : bond 0.04550 / 3.00 ( 474) hydrogen bonds : angle 4.34796 / 3.11 ( 1350) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8579 (mtm-85) cc_final: 0.7814 (mtm-85) REVERT: A 27 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8746 (tp30) REVERT: A 31 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8554 (mm-40) REVERT: B 12 GLU cc_start: 0.8976 (tp30) cc_final: 0.8344 (tp30) REVERT: B 215 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7600 (pp20) REVERT: B 254 ASP cc_start: 0.8504 (t70) cc_final: 0.8195 (t0) REVERT: G 46 LYS cc_start: 0.9426 (mtmm) cc_final: 0.9215 (mppt) REVERT: N 3 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8431 (mm-40) REVERT: N 5 GLN cc_start: 0.8494 (mt0) cc_final: 0.8185 (mp10) REVERT: N 46 GLU cc_start: 0.8811 (tt0) cc_final: 0.8371 (tt0) REVERT: N 95 TYR cc_start: 0.8963 (m-80) cc_final: 0.8745 (m-80) REVERT: P 11 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8683 (mmmm) REVERT: P 20 ARG cc_start: 0.8966 (ttp80) cc_final: 0.8438 (ttp80) REVERT: R 180 GLU cc_start: 0.8624 (pm20) cc_final: 0.8205 (pm20) REVERT: R 185 ASP cc_start: 0.8946 (m-30) cc_final: 0.8470 (m-30) REVERT: R 469 GLU cc_start: 0.8993 (tp30) cc_final: 0.8648 (tm-30) outliers start: 19 outliers final: 8 residues processed: 148 average time/residue: 0.7307 time to fit residues: 114.2163 Evaluate side-chains 139 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 281 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 8 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.086629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.062230 restraints weight = 21835.720| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.09 r_work: 0.2774 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9251 Z= 0.129 Angle : 0.648 11.114 12558 Z= 0.337 Chirality : 0.042 0.168 1394 Planarity : 0.004 0.063 1607 Dihedral : 4.314 32.628 1269 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.86 % Allowed : 20.99 % Favored : 78.16 % Cbeta Deviations : 0.28 % 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: 1.10 (0.26), residues: 1130 helix: 1.87 (0.25), residues: 445 sheet: 0.33 (0.34), residues: 229 loop : -0.12 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 13 TYR 0.021 0.001 TYR R 191 PHE 0.015 0.001 PHE R 315 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.000 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9245) covalent geometry : angle 0.64764 / 0.34 (12546) SS BOND : bond 0.00149 / 0.07 ( 6) SS BOND : angle 0.64283 / 0.42 ( 12) hydrogen bonds : bond 0.04070 / 2.68 ( 474) hydrogen bonds : angle 4.25192 / 3.06 ( 1350) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8583 (mtm-85) cc_final: 0.7846 (mtm-85) REVERT: A 27 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8720 (tp30) REVERT: A 31 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8509 (mm-40) REVERT: B 12 GLU cc_start: 0.8942 (tp30) cc_final: 0.8281 (tp30) REVERT: B 197 ARG cc_start: 0.8730 (mmm160) cc_final: 0.8286 (mmm160) REVERT: B 215 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7580 (pp20) REVERT: B 254 ASP cc_start: 0.8465 (t70) cc_final: 0.8179 (t0) REVERT: G 21 MET cc_start: 0.9388 (tpp) cc_final: 0.8829 (mpp) REVERT: N 3 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8155 (tp40) REVERT: N 43 LYS cc_start: 0.8394 (mtpt) cc_final: 0.8097 (mmmm) REVERT: N 46 GLU cc_start: 0.8757 (tt0) cc_final: 0.8333 (tt0) REVERT: N 76 LYS cc_start: 0.9616 (mtpp) cc_final: 0.9234 (mtmm) REVERT: P 11 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8589 (mmmm) REVERT: P 20 ARG cc_start: 0.8997 (ttp80) cc_final: 0.8242 (ttp80) REVERT: P 21 ARG cc_start: 0.8422 (ppt170) cc_final: 0.8127 (ppt90) REVERT: R 136 TYR cc_start: 0.8922 (t80) cc_final: 0.8378 (t80) REVERT: R 180 GLU cc_start: 0.8584 (pm20) cc_final: 0.8175 (pm20) REVERT: R 185 ASP cc_start: 0.8942 (m-30) cc_final: 0.8469 (m-30) REVERT: R 469 GLU cc_start: 0.8968 (tp30) cc_final: 0.8650 (tm-30) outliers start: 8 outliers final: 5 residues processed: 144 average time/residue: 0.7206 time to fit residues: 109.3611 Evaluate side-chains 144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 281 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 82 optimal weight: 40.0000 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.0470 chunk 25 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN N 120 GLN ** R 401 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 = 0.3433 r_free = 0.3433 target = 0.086649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.062632 restraints weight = 21777.456| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.07 r_work: 0.2783 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9251 Z= 0.133 Angle : 0.668 12.656 12558 Z= 0.342 Chirality : 0.042 0.154 1394 Planarity : 0.004 0.063 1607 Dihedral : 4.273 32.654 1269 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.18 % Allowed : 20.56 % Favored : 78.27 % Cbeta Deviations : 0.28 % 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 (0.26), residues: 1130 helix: 1.91 (0.25), residues: 441 sheet: 0.33 (0.34), residues: 229 loop : -0.11 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 134 TYR 0.021 0.001 TYR R 191 PHE 0.014 0.001 PHE R 315 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.000 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9245) covalent geometry : angle 0.66764 / 0.34 (12546) SS BOND : bond 0.00148 / 0.07 ( 6) SS BOND : angle 0.64067 / 0.41 ( 12) hydrogen bonds : bond 0.04010 / 2.64 ( 474) hydrogen bonds : angle 4.22937 / 3.03 ( 1350) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3251.29 seconds wall clock time: 56 minutes 26.50 seconds (3386.50 seconds total)