Starting phenix.real_space_refine on Sun Apr 5 12:12:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lb8_23251/04_2026/7lb8_23251.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lb8_23251/04_2026/7lb8_23251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lb8_23251/04_2026/7lb8_23251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lb8_23251/04_2026/7lb8_23251.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lb8_23251/04_2026/7lb8_23251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lb8_23251/04_2026/7lb8_23251.map" } resolution = 3.4 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= 0.003 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 64 5.16 5 C 6779 2.51 5 N 1785 2.21 5 O 1811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10439 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4610 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 30, 'TRANS': 599} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 3, 'PHE:plan': 1, 'TRP:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "D" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2085 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 20, 'TRANS': 244} Chain: "U" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1896 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 17, 'TRANS': 237} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 17, 'TRANS': 237} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 6, 'HIS:plan': 3, 'GLU:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Residues with excluded nonbonded symmetry interactions: 35 residue: pdb=" N ILE B 111 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 111 " occ=0.00 residue: pdb=" N PRO B 112 " occ=0.00 ... (3 atoms not shown) pdb=" CB PRO B 112 " occ=0.00 residue: pdb=" N GLY B 113 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 113 " occ=0.00 residue: pdb=" N VAL B 135 " occ=0.00 ... (3 atoms not shown) pdb=" CB VAL B 135 " occ=0.00 residue: pdb=" N ALA B 136 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA B 136 " occ=0.00 residue: pdb=" N TRP B 137 " occ=0.00 ... (3 atoms not shown) pdb=" CB TRP B 137 " occ=0.00 residue: pdb=" N GLY B 138 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 138 " occ=0.00 residue: pdb=" N LEU B 217 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 217 " occ=0.00 residue: pdb=" N ASP B 218 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP B 218 " occ=0.00 residue: pdb=" N ASP B 219 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP B 219 " occ=0.00 residue: pdb=" N TRP B 449 " occ=0.00 ... (3 atoms not shown) pdb=" CB TRP B 449 " occ=0.00 residue: pdb=" N LEU B 450 " occ=0.00 ... (3 atoms not shown) pdb=" CB LEU B 450 " occ=0.00 ... (remaining 23 not shown) Time building chain proxies: 2.52, per 1000 atoms: 0.24 Number of scatterers: 10439 At special positions: 0 Unit cell: (81.498, 95.88, 140.624, 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 64 16.00 O 1811 8.00 N 1785 7.00 C 6779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.85 Conformation dependent library (CDL) restraints added in 561.4 milliseconds 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 8 sheets defined 61.3% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 6 through 32 Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 36 through 42 Processing helix chain 'B' and resid 49 through 54 removed outlier: 3.550A pdb=" N PHE B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 83 Proline residue: B 60 - end of helix removed outlier: 3.551A pdb=" N LEU B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 108 removed outlier: 3.813A pdb=" N LEU B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 134 removed outlier: 3.533A pdb=" N GLN B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 168 Processing helix chain 'B' and resid 172 through 179 Processing helix chain 'B' and resid 188 through 207 Proline residue: B 196 - end of helix Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.555A pdb=" N LEU B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 228 through 251 Processing helix chain 'B' and resid 256 through 259 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 272 through 302 removed outlier: 3.697A pdb=" N ARG B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 323 Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 349 through 370 Processing helix chain 'B' and resid 380 through 387 removed outlier: 3.753A pdb=" N ASP B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 416 Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 426 through 442 Processing helix chain 'B' and resid 454 through 473 removed outlier: 3.511A pdb=" N GLY B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 500 removed outlier: 3.528A pdb=" N SER B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 513 Processing helix chain 'B' and resid 520 through 538 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.593A pdb=" N ARG B 556 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 584 removed outlier: 3.760A pdb=" N ALA B 568 " --> pdb=" O PRO B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 602 Proline residue: B 595 - end of helix removed outlier: 3.759A pdb=" N GLY B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 631 Processing helix chain 'B' and resid 638 through 658 removed outlier: 3.697A pdb=" N LEU B 642 " --> pdb=" O PRO B 638 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) Proline residue: B 649 - end of helix Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 42 through 53 Processing helix chain 'D' and resid 61 through 69 removed outlier: 3.623A pdb=" N TYR D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 95 Processing helix chain 'D' and resid 109 through 115 Processing helix chain 'D' and resid 129 through 146 removed outlier: 3.702A pdb=" N MET D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.518A pdb=" N MET D 165 " --> pdb=" O PHE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.780A pdb=" N VAL D 170 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 204 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.513A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 293 Processing helix chain 'U' and resid 49 through 58 removed outlier: 3.947A pdb=" N LEU U 53 " --> pdb=" O GLY U 49 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU U 54 " --> pdb=" O LYS U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 86 Processing helix chain 'U' and resid 101 through 109 Processing helix chain 'U' and resid 110 through 115 removed outlier: 4.136A pdb=" N HIS U 114 " --> pdb=" O ARG U 110 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 135 removed outlier: 3.725A pdb=" N VAL U 128 " --> pdb=" O ASP U 124 " (cutoff:3.500A) Processing helix chain 'U' and resid 149 through 164 Processing helix chain 'U' and resid 179 through 198 Processing helix chain 'U' and resid 207 through 214 Processing helix chain 'U' and resid 236 through 246 removed outlier: 4.196A pdb=" N GLU U 242 " --> pdb=" O GLY U 238 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET U 243 " --> pdb=" O GLU U 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 49 through 58 Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.508A pdb=" N GLU C 129 " --> pdb=" O ARG C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 165 removed outlier: 3.758A pdb=" N ARG C 155 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 161 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 197 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 237 through 246 Processing sheet with id=AA1, first strand: chain 'D' and resid 79 through 80 removed outlier: 3.746A pdb=" N GLY D 58 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE D 122 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TRP D 102 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 220 through 223 removed outlier: 6.710A pdb=" N HIS D 187 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 183 " --> pdb=" O HIS D 187 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU D 178 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE D 238 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N THR D 180 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL D 235 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL D 269 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N CYS D 237 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 30 through 33 removed outlier: 4.344A pdb=" N ALA U 13 " --> pdb=" O LEU U 69 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU U 69 " --> pdb=" O ALA U 13 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'U' and resid 87 through 89 removed outlier: 6.271A pdb=" N ALA U 88 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL U 39 " --> pdb=" O TYR U 217 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL U 219 " --> pdb=" O VAL U 39 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLY U 41 " --> pdb=" O VAL U 219 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA U 228 " --> pdb=" O ALA U 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'U' and resid 250 through 252 Processing sheet with id=AA6, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 90 removed outlier: 5.935A pdb=" N ALA C 88 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASP C 172 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU C 90 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 169 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL C 204 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU C 171 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL C 219 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLY C 41 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU C 221 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE C 43 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 249 through 252 598 hydrogen bonds defined for protein. 1749 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: 1.64 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3367 1.34 - 1.46: 2164 1.46 - 1.58: 5023 1.58 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 10671 Sorted by residual: bond pdb=" CA LEU B 550 " pdb=" C LEU B 550 " ideal model delta sigma weight residual 1.525 1.571 -0.045 1.40e-02 5.10e+03 1.04e+01 bond pdb=" N PRO B 549 " pdb=" CD PRO B 549 " ideal model delta sigma weight residual 1.473 1.506 -0.033 1.40e-02 5.10e+03 5.47e+00 bond pdb=" N PRO B 549 " pdb=" CA PRO B 549 " ideal model delta sigma weight residual 1.467 1.483 -0.016 1.21e-02 6.83e+03 1.70e+00 bond pdb=" N LEU B 550 " pdb=" CA LEU B 550 " ideal model delta sigma weight residual 1.461 1.480 -0.018 1.49e-02 4.50e+03 1.49e+00 bond pdb=" CA ALA U 72 " pdb=" C ALA U 72 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.30e-02 5.92e+03 1.32e+00 ... (remaining 10666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 14337 2.04 - 4.09: 168 4.09 - 6.13: 42 6.13 - 8.18: 11 8.18 - 10.22: 3 Bond angle restraints: 14561 Sorted by residual: angle pdb=" C PRO B 549 " pdb=" CA PRO B 549 " pdb=" CB PRO B 549 " ideal model delta sigma weight residual 111.21 100.99 10.22 1.33e+00 5.65e-01 5.91e+01 angle pdb=" N LEU B 550 " pdb=" CA LEU B 550 " pdb=" CB LEU B 550 " ideal model delta sigma weight residual 112.30 103.05 9.25 1.52e+00 4.33e-01 3.70e+01 angle pdb=" N LEU B 550 " pdb=" CA LEU B 550 " pdb=" C LEU B 550 " ideal model delta sigma weight residual 112.24 118.73 -6.49 1.28e+00 6.10e-01 2.57e+01 angle pdb=" N LEU B 548 " pdb=" CA LEU B 548 " pdb=" C LEU B 548 " ideal model delta sigma weight residual 113.16 106.36 6.80 1.42e+00 4.96e-01 2.29e+01 angle pdb=" N GLY B 551 " pdb=" CA GLY B 551 " pdb=" C GLY B 551 " ideal model delta sigma weight residual 113.18 121.39 -8.21 2.37e+00 1.78e-01 1.20e+01 ... (remaining 14556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5621 17.97 - 35.95: 531 35.95 - 53.92: 124 53.92 - 71.90: 15 71.90 - 89.87: 8 Dihedral angle restraints: 6299 sinusoidal: 2319 harmonic: 3980 Sorted by residual: dihedral pdb=" C PRO B 549 " pdb=" N PRO B 549 " pdb=" CA PRO B 549 " pdb=" CB PRO B 549 " ideal model delta harmonic sigma weight residual -120.70 -107.88 -12.82 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" CB GLU U 65 " pdb=" CG GLU U 65 " pdb=" CD GLU U 65 " pdb=" OE1 GLU U 65 " ideal model delta sinusoidal sigma weight residual 0.00 89.87 -89.87 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASN U 16 " pdb=" CB ASN U 16 " pdb=" CG ASN U 16 " pdb=" OD1 ASN U 16 " ideal model delta sinusoidal sigma weight residual -90.00 -158.21 68.21 2 2.00e+01 2.50e-03 1.03e+01 ... (remaining 6296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1327 0.043 - 0.086: 330 0.086 - 0.128: 81 0.128 - 0.171: 4 0.171 - 0.214: 1 Chirality restraints: 1743 Sorted by residual: chirality pdb=" CA PRO B 549 " pdb=" N PRO B 549 " pdb=" C PRO B 549 " pdb=" CB PRO B 549 " both_signs ideal model delta sigma weight residual False 2.72 2.93 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE U 247 " pdb=" CA ILE U 247 " pdb=" CG1 ILE U 247 " pdb=" CG2 ILE U 247 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA ILE C 251 " pdb=" N ILE C 251 " pdb=" C ILE C 251 " pdb=" CB ILE C 251 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 1740 not shown) Planarity restraints: 1827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 548 " -0.043 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PRO B 549 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 549 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 549 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 550 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C LEU B 550 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU B 550 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY B 551 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 44 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO D 45 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 45 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 45 " 0.024 5.00e-02 4.00e+02 ... (remaining 1824 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 118 2.65 - 3.22: 9889 3.22 - 3.78: 16347 3.78 - 4.34: 21405 4.34 - 4.90: 35357 Nonbonded interactions: 83116 Sorted by model distance: nonbonded pdb=" O PRO B 549 " pdb=" CG LEU B 550 " model vdw 2.093 3.470 nonbonded pdb=" O ILE B 103 " pdb=" OG1 THR B 107 " model vdw 2.193 3.040 nonbonded pdb=" OG1 THR C 231 " pdb=" OE2 GLU C 234 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR U 217 " pdb=" OE1 GLN U 229 " model vdw 2.215 3.040 nonbonded pdb=" O THR B 546 " pdb=" CG PRO B 549 " model vdw 2.235 3.440 ... (remaining 83111 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 'C' and (resid 11 through 72 or (resid 73 through 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 137 or (resid 138 and ( \ name N or name CA or name C or name O or name CB )) or resid 139 or (resid 140 t \ hrough 141 and (name N or name CA or name C or name O or name CB )) or resid 142 \ through 265)) selection = (chain 'U' and (resid 11 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 or (resid 22 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 23 through 25 and (name N or name CA or na \ me C or name O or name CB )) or resid 26 or (resid 27 through 28 and (name N or \ name CA or name C or name O or name CB )) or resid 29 through 37 or (resid 38 an \ d (name N or name CA or name C or name O or name CB )) or resid 39 through 59 or \ (resid 60 and (name N or name CA or name C or name O or name CB )) or resid 61 \ through 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) \ or resid 95 through 118 or (resid 119 through 120 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 121 through 125 and (name N or name CA or \ name C or name O or name CB )) or resid 126 through 195 or (resid 196 and (name \ N or name CA or name C or name O or name CB )) or resid 197 through 247 or (resi \ d 248 and (name N or name CA or name C or name O or name CB )) or resid 249 thro \ ugh 259 or (resid 260 and (name N or name CA or name C or name O or name CB )) o \ r resid 261 through 265)) } 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=0.00 max=1.00 mean=0.98 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.830 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 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 : 0.002 0.045 10671 Z= 0.125 Angle : 0.620 10.221 14561 Z= 0.328 Chirality : 0.039 0.214 1743 Planarity : 0.004 0.063 1827 Dihedral : 14.950 89.874 3743 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.73 % Favored : 94.98 % Rotamer: Outliers : 2.66 % Allowed : 23.36 % Favored : 73.98 % Cbeta Deviations : 0.08 % 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: -1.98 (0.20), residues: 1395 helix: -0.21 (0.17), residues: 796 sheet: -2.06 (0.41), residues: 97 loop : -2.96 (0.22), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 213 TYR 0.014 0.001 TYR U 245 PHE 0.024 0.001 PHE B 589 TRP 0.007 0.001 TRP B 195 HIS 0.004 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00234 (10671) covalent geometry : angle 0.61963 (14561) hydrogen bonds : bond 0.12912 ( 598) hydrogen bonds : angle 5.70696 ( 1749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.377 Fit side-chains REVERT: B 147 ILE cc_start: 0.7801 (mt) cc_final: 0.7523 (mt) REVERT: B 288 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.5957 (tt) REVERT: B 493 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6721 (mt) REVERT: B 495 MET cc_start: 0.7495 (mmm) cc_final: 0.6510 (mtt) REVERT: B 593 MET cc_start: 0.5923 (mmt) cc_final: 0.5702 (mmt) REVERT: B 607 MET cc_start: 0.8129 (tpp) cc_final: 0.7844 (tpp) REVERT: B 657 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6862 (mtmt) REVERT: D 288 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7889 (mp) REVERT: U 53 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7240 (tm) REVERT: U 57 LEU cc_start: 0.6060 (tp) cc_final: 0.5724 (tp) REVERT: U 100 MET cc_start: 0.3827 (tpt) cc_final: 0.3530 (mmp) REVERT: U 129 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7377 (tp30) REVERT: U 226 MET cc_start: 0.3299 (tpt) cc_final: 0.2278 (tmm) REVERT: C 65 GLU cc_start: 0.6397 (mt-10) cc_final: 0.5050 (tp30) REVERT: C 167 ARG cc_start: 0.6878 (mmp80) cc_final: 0.5178 (ttp80) outliers start: 28 outliers final: 10 residues processed: 247 average time/residue: 0.1143 time to fit residues: 38.7542 Evaluate side-chains 191 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 180 ILE Chi-restraints excluded: chain U residue 216 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN B 171 GLN U 16 ASN C 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.230861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.215960 restraints weight = 11661.221| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 0.60 r_work: 0.4061 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10671 Z= 0.129 Angle : 0.608 11.739 14561 Z= 0.290 Chirality : 0.042 0.203 1743 Planarity : 0.005 0.049 1827 Dihedral : 5.484 59.172 1521 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.37 % Favored : 96.49 % Rotamer: Outliers : 3.13 % Allowed : 22.41 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.71 (0.22), residues: 1395 helix: 0.88 (0.19), residues: 786 sheet: -1.48 (0.45), residues: 102 loop : -2.48 (0.23), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 556 TYR 0.013 0.001 TYR C 214 PHE 0.032 0.002 PHE U 120 TRP 0.011 0.001 TRP B 195 HIS 0.007 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00297 (10671) covalent geometry : angle 0.60831 (14561) hydrogen bonds : bond 0.03244 ( 598) hydrogen bonds : angle 4.29585 ( 1749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.343 Fit side-chains REVERT: B 288 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6709 (tt) REVERT: B 495 MET cc_start: 0.8022 (mmm) cc_final: 0.7239 (mtt) REVERT: D 288 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8224 (mp) REVERT: U 53 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7144 (tm) REVERT: U 57 LEU cc_start: 0.6009 (tp) cc_final: 0.5526 (tp) REVERT: U 210 MET cc_start: 0.7303 (mmp) cc_final: 0.6706 (mmt) REVERT: C 65 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6072 (tp30) REVERT: C 167 ARG cc_start: 0.6568 (mmp80) cc_final: 0.5791 (ttp80) outliers start: 33 outliers final: 23 residues processed: 225 average time/residue: 0.0968 time to fit residues: 31.3388 Evaluate side-chains 199 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 chunk 39 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN D 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.217258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.205088 restraints weight = 11597.364| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 0.48 r_work: 0.4048 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10671 Z= 0.168 Angle : 0.649 10.608 14561 Z= 0.312 Chirality : 0.044 0.319 1743 Planarity : 0.005 0.048 1827 Dihedral : 5.465 55.784 1508 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 5.41 % Allowed : 22.41 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.43 (0.22), residues: 1395 helix: 1.05 (0.19), residues: 783 sheet: -1.59 (0.42), residues: 118 loop : -2.17 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 556 TYR 0.024 0.002 TYR C 214 PHE 0.021 0.002 PHE B 54 TRP 0.014 0.001 TRP B 195 HIS 0.008 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00399 (10671) covalent geometry : angle 0.64948 (14561) hydrogen bonds : bond 0.03682 ( 598) hydrogen bonds : angle 4.35917 ( 1749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 184 time to evaluate : 0.347 Fit side-chains REVERT: B 384 ASP cc_start: 0.7621 (m-30) cc_final: 0.7158 (m-30) REVERT: B 395 MET cc_start: 0.7832 (tpp) cc_final: 0.7552 (mmt) REVERT: B 480 LEU cc_start: 0.8825 (tt) cc_final: 0.8618 (tt) REVERT: B 495 MET cc_start: 0.8130 (mmm) cc_final: 0.7506 (mtt) REVERT: B 529 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8295 (mp) REVERT: B 593 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.6558 (mmt) REVERT: B 600 MET cc_start: 0.6908 (mtm) cc_final: 0.6696 (ptp) REVERT: D 79 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8202 (mt) REVERT: U 53 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7125 (tm) REVERT: U 57 LEU cc_start: 0.5822 (tp) cc_final: 0.5128 (tp) REVERT: U 210 MET cc_start: 0.7307 (mmp) cc_final: 0.6852 (mmt) REVERT: C 65 GLU cc_start: 0.6540 (mt-10) cc_final: 0.6126 (tp30) outliers start: 57 outliers final: 32 residues processed: 227 average time/residue: 0.0880 time to fit residues: 29.6254 Evaluate side-chains 208 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain U residue 186 VAL Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain U residue 249 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 184 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 91 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.222447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.205484 restraints weight = 11706.684| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 0.60 r_work: 0.3966 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10671 Z= 0.128 Angle : 0.621 15.236 14561 Z= 0.293 Chirality : 0.042 0.261 1743 Planarity : 0.005 0.051 1827 Dihedral : 5.160 54.950 1504 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.09 % Favored : 95.84 % Rotamer: Outliers : 4.08 % Allowed : 24.12 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.17 (0.22), residues: 1395 helix: 1.25 (0.19), residues: 787 sheet: -1.49 (0.43), residues: 118 loop : -2.06 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 526 TYR 0.013 0.001 TYR C 214 PHE 0.032 0.002 PHE U 120 TRP 0.018 0.001 TRP B 389 HIS 0.007 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00303 (10671) covalent geometry : angle 0.62112 (14561) hydrogen bonds : bond 0.03187 ( 598) hydrogen bonds : angle 4.25000 ( 1749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.362 Fit side-chains REVERT: B 384 ASP cc_start: 0.7752 (m-30) cc_final: 0.7338 (m-30) REVERT: B 495 MET cc_start: 0.8061 (mmm) cc_final: 0.7325 (mtt) REVERT: B 593 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6885 (mmt) REVERT: U 53 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7282 (tm) REVERT: U 57 LEU cc_start: 0.6213 (tp) cc_final: 0.5536 (tp) REVERT: U 210 MET cc_start: 0.7402 (mmp) cc_final: 0.6794 (mmt) REVERT: C 65 GLU cc_start: 0.6456 (mt-10) cc_final: 0.5891 (tp30) outliers start: 43 outliers final: 28 residues processed: 216 average time/residue: 0.0791 time to fit residues: 26.2724 Evaluate side-chains 200 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 235 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 42 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 7 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.223725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.213221 restraints weight = 11766.137| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 0.46 r_work: 0.4142 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10671 Z= 0.113 Angle : 0.597 11.529 14561 Z= 0.280 Chirality : 0.041 0.205 1743 Planarity : 0.005 0.051 1827 Dihedral : 5.038 57.525 1504 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.70 % Rotamer: Outliers : 3.99 % Allowed : 25.26 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.23), residues: 1395 helix: 1.39 (0.19), residues: 793 sheet: -1.05 (0.43), residues: 130 loop : -2.10 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 526 TYR 0.012 0.001 TYR C 214 PHE 0.029 0.001 PHE B 433 TRP 0.013 0.001 TRP B 389 HIS 0.007 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00258 (10671) covalent geometry : angle 0.59703 (14561) hydrogen bonds : bond 0.03004 ( 598) hydrogen bonds : angle 4.14845 ( 1749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.387 Fit side-chains REVERT: B 384 ASP cc_start: 0.7957 (m-30) cc_final: 0.7491 (m-30) REVERT: B 495 MET cc_start: 0.8103 (mmm) cc_final: 0.7312 (mtt) REVERT: B 525 TRP cc_start: 0.7017 (t60) cc_final: 0.6706 (m100) REVERT: B 593 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6923 (mmt) REVERT: D 213 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7040 (pm20) REVERT: U 53 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7390 (tm) REVERT: U 57 LEU cc_start: 0.6378 (tp) cc_final: 0.5788 (tp) REVERT: U 210 MET cc_start: 0.7502 (mmp) cc_final: 0.6799 (mmt) REVERT: U 226 MET cc_start: 0.3694 (tmm) cc_final: 0.3461 (tmm) REVERT: C 65 GLU cc_start: 0.6467 (mt-10) cc_final: 0.5880 (tp30) outliers start: 42 outliers final: 30 residues processed: 212 average time/residue: 0.0840 time to fit residues: 26.9406 Evaluate side-chains 203 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 144 LEU Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 235 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 126 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.211089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.198316 restraints weight = 11750.584| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 0.49 r_work: 0.3976 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10671 Z= 0.219 Angle : 0.703 13.168 14561 Z= 0.340 Chirality : 0.046 0.289 1743 Planarity : 0.005 0.053 1827 Dihedral : 5.660 54.792 1504 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.59 % Favored : 95.27 % Rotamer: Outliers : 5.79 % Allowed : 23.74 % Favored : 70.47 % 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 (0.22), residues: 1395 helix: 0.97 (0.19), residues: 789 sheet: -1.10 (0.43), residues: 130 loop : -2.20 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 526 TYR 0.021 0.002 TYR C 214 PHE 0.032 0.002 PHE B 433 TRP 0.012 0.002 TRP D 68 HIS 0.008 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00537 (10671) covalent geometry : angle 0.70313 (14561) hydrogen bonds : bond 0.03936 ( 598) hydrogen bonds : angle 4.58379 ( 1749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 0.278 Fit side-chains REVERT: B 153 VAL cc_start: 0.7446 (t) cc_final: 0.7238 (p) REVERT: B 192 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7612 (mm-30) REVERT: B 376 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8601 (t) REVERT: B 384 ASP cc_start: 0.8198 (m-30) cc_final: 0.7729 (m-30) REVERT: B 466 MET cc_start: 0.8415 (tpt) cc_final: 0.7981 (tpt) REVERT: B 495 MET cc_start: 0.8811 (mmm) cc_final: 0.7988 (mtt) REVERT: U 53 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7444 (tm) REVERT: U 57 LEU cc_start: 0.6574 (tp) cc_final: 0.6133 (tp) REVERT: U 185 ASP cc_start: 0.7563 (t0) cc_final: 0.6907 (m-30) REVERT: C 65 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6039 (tp30) outliers start: 61 outliers final: 41 residues processed: 225 average time/residue: 0.0753 time to fit residues: 25.9799 Evaluate side-chains 211 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 43 ILE Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 235 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 183 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 = 0.4305 r_free = 0.4305 target = 0.215812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.203420 restraints weight = 11532.377| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 0.47 r_work: 0.4017 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3867 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10671 Z= 0.126 Angle : 0.646 15.047 14561 Z= 0.301 Chirality : 0.041 0.219 1743 Planarity : 0.005 0.052 1827 Dihedral : 5.363 57.871 1504 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.91 % Rotamer: Outliers : 4.46 % Allowed : 25.26 % Favored : 70.28 % 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: -0.19 (0.22), residues: 1395 helix: 1.17 (0.19), residues: 793 sheet: -0.93 (0.43), residues: 130 loop : -2.16 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 526 TYR 0.018 0.001 TYR C 214 PHE 0.029 0.001 PHE B 433 TRP 0.016 0.001 TRP B 195 HIS 0.007 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00293 (10671) covalent geometry : angle 0.64612 (14561) hydrogen bonds : bond 0.03245 ( 598) hydrogen bonds : angle 4.34409 ( 1749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.347 Fit side-chains REVERT: B 56 TYR cc_start: 0.6371 (OUTLIER) cc_final: 0.5328 (t80) REVERT: B 192 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7602 (mm-30) REVERT: B 376 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8530 (t) REVERT: B 384 ASP cc_start: 0.8102 (m-30) cc_final: 0.7697 (m-30) REVERT: B 466 MET cc_start: 0.8275 (tpt) cc_final: 0.7786 (tpt) REVERT: B 495 MET cc_start: 0.8607 (mmm) cc_final: 0.7695 (mtt) REVERT: B 525 TRP cc_start: 0.7036 (t60) cc_final: 0.6786 (m100) REVERT: B 531 MET cc_start: 0.7595 (ttt) cc_final: 0.7389 (ttt) REVERT: U 53 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7458 (tm) REVERT: U 57 LEU cc_start: 0.6475 (tp) cc_final: 0.6007 (tp) REVERT: U 185 ASP cc_start: 0.7351 (t0) cc_final: 0.6636 (m-30) REVERT: U 206 HIS cc_start: 0.5754 (OUTLIER) cc_final: 0.4965 (m-70) REVERT: C 65 GLU cc_start: 0.6445 (mt-10) cc_final: 0.5995 (tp30) outliers start: 47 outliers final: 36 residues processed: 209 average time/residue: 0.0794 time to fit residues: 25.2109 Evaluate side-chains 208 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 645 PHE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain U residue 43 ILE Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 189 LEU Chi-restraints excluded: chain U residue 206 HIS Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 235 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 87 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 68 optimal weight: 0.4980 chunk 129 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 183 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 = 0.4310 r_free = 0.4310 target = 0.216266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.205968 restraints weight = 11579.599| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 0.46 r_work: 0.4056 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10671 Z= 0.126 Angle : 0.635 12.655 14561 Z= 0.296 Chirality : 0.042 0.237 1743 Planarity : 0.005 0.051 1827 Dihedral : 5.220 58.306 1504 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.37 % Favored : 95.48 % Rotamer: Outliers : 4.65 % Allowed : 25.26 % Favored : 70.09 % 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: -0.05 (0.23), residues: 1395 helix: 1.29 (0.19), residues: 793 sheet: -0.88 (0.43), residues: 130 loop : -2.12 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 526 TYR 0.016 0.001 TYR C 214 PHE 0.026 0.001 PHE B 433 TRP 0.017 0.001 TRP B 195 HIS 0.007 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00295 (10671) covalent geometry : angle 0.63474 (14561) hydrogen bonds : bond 0.03161 ( 598) hydrogen bonds : angle 4.29639 ( 1749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.395 Fit side-chains REVERT: B 56 TYR cc_start: 0.6297 (OUTLIER) cc_final: 0.5378 (t80) REVERT: B 192 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7481 (mm-30) REVERT: B 384 ASP cc_start: 0.7978 (m-30) cc_final: 0.7620 (m-30) REVERT: B 466 MET cc_start: 0.8214 (tpt) cc_final: 0.7773 (tpt) REVERT: B 495 MET cc_start: 0.8439 (mmm) cc_final: 0.7567 (mtt) REVERT: U 53 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7348 (tm) REVERT: U 57 LEU cc_start: 0.6293 (tp) cc_final: 0.5857 (tp) REVERT: C 65 GLU cc_start: 0.6466 (mt-10) cc_final: 0.6156 (tp30) outliers start: 49 outliers final: 40 residues processed: 212 average time/residue: 0.0795 time to fit residues: 25.7488 Evaluate side-chains 209 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 645 PHE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 43 ILE Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 189 LEU Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 184 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 54 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 0.0670 chunk 128 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 86 optimal weight: 0.0000 chunk 37 optimal weight: 1.9990 overall best weight: 0.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.214227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.196804 restraints weight = 11637.791| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 0.68 r_work: 0.3922 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10671 Z= 0.109 Angle : 0.629 13.562 14561 Z= 0.290 Chirality : 0.041 0.227 1743 Planarity : 0.005 0.052 1827 Dihedral : 5.014 55.104 1504 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.99 % Rotamer: Outliers : 3.61 % Allowed : 26.88 % Favored : 69.52 % 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: 0.12 (0.23), residues: 1395 helix: 1.44 (0.19), residues: 793 sheet: -0.80 (0.44), residues: 130 loop : -2.08 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 526 TYR 0.014 0.001 TYR C 214 PHE 0.026 0.001 PHE B 433 TRP 0.015 0.001 TRP B 195 HIS 0.007 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00245 (10671) covalent geometry : angle 0.62938 (14561) hydrogen bonds : bond 0.02956 ( 598) hydrogen bonds : angle 4.20940 ( 1749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.386 Fit side-chains REVERT: B 56 TYR cc_start: 0.6239 (OUTLIER) cc_final: 0.5318 (t80) REVERT: B 192 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7278 (mm-30) REVERT: B 384 ASP cc_start: 0.7878 (m-30) cc_final: 0.7508 (m-30) REVERT: B 466 MET cc_start: 0.8117 (tpt) cc_final: 0.7555 (tpt) REVERT: B 492 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7513 (mmp) REVERT: B 495 MET cc_start: 0.8197 (mmm) cc_final: 0.7313 (mtt) REVERT: U 30 LEU cc_start: 0.7024 (pt) cc_final: 0.5757 (tp) REVERT: U 53 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7337 (tm) REVERT: U 57 LEU cc_start: 0.6238 (tp) cc_final: 0.5784 (tp) REVERT: U 206 HIS cc_start: 0.5692 (OUTLIER) cc_final: 0.4917 (m-70) REVERT: U 236 MET cc_start: 0.6825 (mmm) cc_final: 0.5370 (pmm) REVERT: C 65 GLU cc_start: 0.6315 (mt-10) cc_final: 0.6029 (tp30) outliers start: 38 outliers final: 29 residues processed: 206 average time/residue: 0.0816 time to fit residues: 25.5442 Evaluate side-chains 203 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 189 LEU Chi-restraints excluded: chain U residue 206 HIS Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 184 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 0.0870 chunk 11 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 183 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 = 0.4288 r_free = 0.4288 target = 0.213055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.196104 restraints weight = 11577.377| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 0.60 r_work: 0.3920 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10671 Z= 0.122 Angle : 0.649 16.202 14561 Z= 0.299 Chirality : 0.041 0.229 1743 Planarity : 0.005 0.052 1827 Dihedral : 4.825 54.828 1501 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.59 % Favored : 95.27 % Rotamer: Outliers : 3.42 % Allowed : 26.88 % Favored : 69.71 % 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: 0.18 (0.23), residues: 1395 helix: 1.48 (0.19), residues: 794 sheet: -0.75 (0.45), residues: 130 loop : -2.04 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 556 TYR 0.015 0.001 TYR C 214 PHE 0.028 0.001 PHE B 433 TRP 0.018 0.001 TRP B 195 HIS 0.007 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00285 (10671) covalent geometry : angle 0.64869 (14561) hydrogen bonds : bond 0.03032 ( 598) hydrogen bonds : angle 4.23211 ( 1749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.558 Fit side-chains REVERT: B 56 TYR cc_start: 0.6337 (OUTLIER) cc_final: 0.5503 (t80) REVERT: B 192 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7256 (mm-30) REVERT: B 384 ASP cc_start: 0.7813 (m-30) cc_final: 0.7488 (m-30) REVERT: B 466 MET cc_start: 0.8131 (tpt) cc_final: 0.7577 (tpt) REVERT: B 495 MET cc_start: 0.8265 (mmm) cc_final: 0.7434 (mmm) REVERT: U 53 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7348 (tm) REVERT: U 57 LEU cc_start: 0.6293 (tp) cc_final: 0.5854 (tp) REVERT: U 206 HIS cc_start: 0.5740 (OUTLIER) cc_final: 0.4968 (m-70) REVERT: U 236 MET cc_start: 0.6779 (mmm) cc_final: 0.5314 (pmm) REVERT: C 65 GLU cc_start: 0.6290 (mt-10) cc_final: 0.6019 (tp30) outliers start: 36 outliers final: 30 residues processed: 197 average time/residue: 0.0779 time to fit residues: 23.0977 Evaluate side-chains 205 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 645 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 189 LEU Chi-restraints excluded: chain U residue 206 HIS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 184 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 114 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 130 optimal weight: 0.3980 chunk 65 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 183 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 = 0.4366 r_free = 0.4366 target = 0.222804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.211073 restraints weight = 11624.474| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 0.47 r_work: 0.4103 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10671 Z= 0.113 Angle : 0.641 16.670 14561 Z= 0.294 Chirality : 0.041 0.218 1743 Planarity : 0.005 0.052 1827 Dihedral : 4.724 55.521 1501 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.20 % Rotamer: Outliers : 3.04 % Allowed : 27.07 % Favored : 69.90 % 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: 0.27 (0.23), residues: 1395 helix: 1.55 (0.19), residues: 795 sheet: -0.71 (0.45), residues: 130 loop : -2.00 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 556 TYR 0.013 0.001 TYR C 214 PHE 0.029 0.001 PHE B 433 TRP 0.017 0.001 TRP B 195 HIS 0.007 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00259 (10671) covalent geometry : angle 0.64138 (14561) hydrogen bonds : bond 0.02928 ( 598) hydrogen bonds : angle 4.17282 ( 1749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2127.08 seconds wall clock time: 37 minutes 12.28 seconds (2232.28 seconds total)