Starting phenix.real_space_refine on Fri Oct 23 14:38:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ycy_72791/10_2026/9ycy_72791.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ycy_72791/10_2026/9ycy_72791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ycy_72791/10_2026/9ycy_72791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ycy_72791/10_2026/9ycy_72791.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ycy_72791/10_2026/9ycy_72791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ycy_72791/10_2026/9ycy_72791.map" } resolution = 2.2 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2063 atoms to isotropic. 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 56 5.16 5 C 5399 2.51 5 N 1430 2.21 5 O 1522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8407 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2476 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 8, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 97 Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 359 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "L" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 63 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2260 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 6, 'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "A" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1562 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 10, 'ASN:plan1': 3, 'ASP:plan': 6, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 95 Chain: "S" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1687 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Time building chain proxies: 1.87, per 1000 atoms: 0.22 Number of scatterers: 8407 At special positions: 0 Unit cell: (89.024, 122.304, 124.8, 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 56 16.00 O 1522 8.00 N 1430 7.00 C 5399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 0.66 Conformation dependent library (CDL) restraints added in 458.5 milliseconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 40.1% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'R' and resid 51 through 55 Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 100 through 119 removed outlier: 3.723A pdb=" N HIS R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 127 Processing helix chain 'R' and resid 136 through 172 Processing helix chain 'R' and resid 175 through 180 Processing helix chain 'R' and resid 181 through 200 Processing helix chain 'R' and resid 201 through 207 removed outlier: 4.014A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 272 Processing helix chain 'R' and resid 295 through 329 Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 365 removed outlier: 3.681A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 370 through 376 removed outlier: 3.695A pdb=" N ILE R 374 " --> pdb=" O ASN R 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.555A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.771A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.881A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.730A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.032A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 329 through 351 removed outlier: 4.087A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.665A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.704A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.611A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.528A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.854A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.700A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.858A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.601A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.679A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 209 through 211 Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.682A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.986A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.344A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 182 through 183 removed outlier: 6.552A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1347 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: 1.38 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2708 1.34 - 1.46: 2102 1.46 - 1.58: 3701 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 8593 Sorted by residual: bond pdb=" CA SER S 196 " pdb=" CB SER S 196 " ideal model delta sigma weight residual 1.537 1.520 0.017 1.45e-02 4.76e+03 1.34e+00 bond pdb=" C GLY S 195 " pdb=" N SER S 196 " ideal model delta sigma weight residual 1.328 1.336 -0.009 8.90e-03 1.26e+04 9.13e-01 bond pdb=" C SER S 196 " pdb=" O SER S 196 " ideal model delta sigma weight residual 1.236 1.227 0.009 9.90e-03 1.02e+04 8.72e-01 bond pdb=" C LEU R 305 " pdb=" O LEU R 305 " ideal model delta sigma weight residual 1.236 1.246 -0.009 1.15e-02 7.56e+03 6.56e-01 bond pdb=" CA PHE R 247 " pdb=" C PHE R 247 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.45e-01 ... (remaining 8588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 11441 1.26 - 2.51: 236 2.51 - 3.77: 41 3.77 - 5.02: 10 5.02 - 6.28: 6 Bond angle restraints: 11734 Sorted by residual: angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.48e+00 angle pdb=" N GLY B 319 " pdb=" CA GLY B 319 " pdb=" C GLY B 319 " ideal model delta sigma weight residual 110.87 114.78 -3.91 1.54e+00 4.22e-01 6.44e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 123.47 127.24 -3.77 1.53e+00 4.27e-01 6.08e+00 angle pdb=" N LYS S 43 " pdb=" CA LYS S 43 " pdb=" C LYS S 43 " ideal model delta sigma weight residual 108.34 111.47 -3.13 1.31e+00 5.83e-01 5.70e+00 angle pdb=" N LYS R 175 " pdb=" CA LYS R 175 " pdb=" C LYS R 175 " ideal model delta sigma weight residual 113.12 110.40 2.72 1.25e+00 6.40e-01 4.74e+00 ... (remaining 11729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4561 17.76 - 35.51: 308 35.51 - 53.27: 77 53.27 - 71.02: 27 71.02 - 88.78: 5 Dihedral angle restraints: 4978 sinusoidal: 1633 harmonic: 3345 Sorted by residual: dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASP S 90 " pdb=" CB ASP S 90 " pdb=" CG ASP S 90 " pdb=" OD1 ASP S 90 " ideal model delta sinusoidal sigma weight residual -30.00 -88.01 58.01 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP S 109 " pdb=" CB ASP S 109 " pdb=" CG ASP S 109 " pdb=" OD1 ASP S 109 " ideal model delta sinusoidal sigma weight residual -30.00 -86.47 56.47 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 4975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 812 0.026 - 0.052: 337 0.052 - 0.078: 139 0.078 - 0.104: 58 0.104 - 0.130: 39 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CA VAL S 187 " pdb=" N VAL S 187 " pdb=" C VAL S 187 " pdb=" CB VAL S 187 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA PRO S 41 " pdb=" N PRO S 41 " pdb=" C PRO S 41 " pdb=" CB PRO S 41 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1382 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO B 236 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 201 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO R 202 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO R 202 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 202 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO S 41 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " 0.018 5.00e-02 4.00e+02 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1727 2.78 - 3.31: 7586 3.31 - 3.84: 14322 3.84 - 4.37: 16538 4.37 - 4.90: 29230 Nonbonded interactions: 69403 Sorted by model distance: nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.250 3.040 nonbonded pdb=" O LEU L 13 " pdb=" OH TYR R 145 " model vdw 2.267 3.040 nonbonded pdb=" NH2 ARG L 9 " pdb=" O ILE R 329 " model vdw 2.351 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.364 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.364 3.040 ... (remaining 69398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.850 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 0.035 8596 Z= 0.114 Angle : 0.491 6.277 11740 Z= 0.280 Chirality : 0.040 0.130 1385 Planarity : 0.003 0.038 1484 Dihedral : 14.140 88.775 2811 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.50 % Allowed : 14.59 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.84 (0.25), residues: 1128 helix: 2.89 (0.25), residues: 407 sheet: 1.19 (0.31), residues: 261 loop : -0.30 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 322 TYR 0.014 0.001 TYR R 145 PHE 0.011 0.001 PHE B 151 TRP 0.009 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 ( 8593) covalent geometry : angle 0.49033 / 0.28 (11734) SS BOND : bond 0.00583 / 0.28 ( 3) SS BOND : angle 1.32761 / 0.73 ( 6) hydrogen bonds : bond 0.16611 / 11.96 ( 477) hydrogen bonds : angle 6.12962 / 4.05 ( 1347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 198 LEU cc_start: 0.4424 (mt) cc_final: 0.4064 (tp) REVERT: R 350 ASN cc_start: 0.3931 (m-40) cc_final: 0.3718 (m-40) REVERT: A 25 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7104 (mp0) outliers start: 4 outliers final: 1 residues processed: 150 average time/residue: 0.4529 time to fit residues: 73.2975 Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 ASN R 126 ASN R 229 HIS A 22 ASN A 256 ASN A 331 ASN S 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.185042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116840 restraints weight = 8179.315| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.98 r_work: 0.3149 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8596 Z= 0.163 Angle : 0.587 8.748 11740 Z= 0.319 Chirality : 0.044 0.160 1385 Planarity : 0.004 0.040 1484 Dihedral : 4.403 20.717 1231 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.01 % Allowed : 14.21 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.87 (0.25), residues: 1128 helix: 2.87 (0.25), residues: 411 sheet: 1.12 (0.31), residues: 280 loop : -0.28 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 322 TYR 0.018 0.002 TYR R 125 PHE 0.023 0.002 PHE R 353 TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 8593) covalent geometry : angle 0.58670 / 0.32 (11734) SS BOND : bond 0.01263 / 0.62 ( 3) SS BOND : angle 1.44808 / 0.80 ( 6) hydrogen bonds : bond 0.05528 / 3.82 ( 477) hydrogen bonds : angle 4.82518 / 3.31 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 153 TYR cc_start: 0.7289 (m-80) cc_final: 0.6825 (m-80) REVERT: R 350 ASN cc_start: 0.6689 (m-40) cc_final: 0.6445 (m-40) REVERT: R 357 SER cc_start: 0.7327 (m) cc_final: 0.7038 (t) REVERT: A 208 ARG cc_start: 0.8353 (ttp80) cc_final: 0.8147 (ttp-110) REVERT: A 354 TYR cc_start: 0.6725 (OUTLIER) cc_final: 0.6295 (t80) outliers start: 16 outliers final: 7 residues processed: 147 average time/residue: 0.4896 time to fit residues: 77.1726 Evaluate side-chains 137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 253 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [15, 87, 2, 19, 68, 72, 46, 102, 30, 3, 10] chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 30 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN C 59 ASN R 104 HIS R 126 ASN A 22 ASN A 255 ASN A 256 ASN A 331 ASN S 3 GLN S 171 GLN S 182 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.187610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124255 restraints weight = 8266.741| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.00 r_work: 0.3211 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8596 Z= 0.110 Angle : 0.490 6.421 11740 Z= 0.269 Chirality : 0.041 0.132 1385 Planarity : 0.003 0.040 1484 Dihedral : 4.046 18.589 1230 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.51 % Allowed : 15.35 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.92 (0.26), residues: 1128 helix: 2.94 (0.26), residues: 412 sheet: 1.26 (0.31), residues: 268 loop : -0.33 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 322 TYR 0.017 0.001 TYR R 125 PHE 0.013 0.001 PHE B 151 TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 ( 8593) covalent geometry : angle 0.48950 / 0.27 (11734) SS BOND : bond 0.00812 / 0.40 ( 3) SS BOND : angle 1.18271 / 0.65 ( 6) hydrogen bonds : bond 0.04390 / 3.01 ( 477) hydrogen bonds : angle 4.49232 / 3.08 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 153 TYR cc_start: 0.7302 (m-80) cc_final: 0.6924 (m-80) REVERT: R 350 ASN cc_start: 0.6667 (m-40) cc_final: 0.6419 (m-40) REVERT: A 208 ARG cc_start: 0.8304 (ttp80) cc_final: 0.8100 (ttp-110) REVERT: A 232 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6690 (pt) outliers start: 12 outliers final: 5 residues processed: 149 average time/residue: 0.4608 time to fit residues: 73.8910 Evaluate side-chains 137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 253 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 309 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [42, 91, 97, 109, 33, 72, 105, 38, 48, 110, 39] chunk 42 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 33 optimal weight: 0.0370 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 ASN R 126 ASN A 22 ASN A 256 ASN A 331 ASN S 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.186854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124834 restraints weight = 8356.861| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.03 r_work: 0.3211 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8596 Z= 0.118 Angle : 0.506 6.659 11740 Z= 0.276 Chirality : 0.042 0.137 1385 Planarity : 0.003 0.041 1484 Dihedral : 4.094 19.112 1230 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.76 % Allowed : 15.60 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.97 (0.26), residues: 1128 helix: 2.91 (0.25), residues: 411 sheet: 1.24 (0.31), residues: 284 loop : -0.25 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 322 TYR 0.014 0.001 TYR S 178 PHE 0.026 0.001 PHE R 353 TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 ( 8593) covalent geometry : angle 0.50579 / 0.28 (11734) SS BOND : bond 0.00918 / 0.45 ( 3) SS BOND : angle 1.27267 / 0.69 ( 6) hydrogen bonds : bond 0.04485 / 3.08 ( 477) hydrogen bonds : angle 4.47445 / 3.07 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 153 TYR cc_start: 0.7316 (m-80) cc_final: 0.6878 (m-80) REVERT: R 353 PHE cc_start: 0.6090 (t80) cc_final: 0.5888 (t80) REVERT: A 208 ARG cc_start: 0.8324 (ttp80) cc_final: 0.8124 (ttp-110) REVERT: A 232 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6742 (pt) REVERT: A 354 TYR cc_start: 0.6769 (OUTLIER) cc_final: 0.6344 (t80) outliers start: 14 outliers final: 8 residues processed: 144 average time/residue: 0.4931 time to fit residues: 76.1283 Evaluate side-chains 144 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 253 SER Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [34, 47, 41, 62, 100, 87, 26, 109, 2, 33, 38] chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN C 59 ASN R 57 ASN R 126 ASN A 22 ASN A 256 ASN A 331 ASN S 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.183349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121774 restraints weight = 8196.970| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.18 r_work: 0.3162 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8596 Z= 0.220 Angle : 0.656 11.405 11740 Z= 0.355 Chirality : 0.047 0.185 1385 Planarity : 0.004 0.041 1484 Dihedral : 4.711 23.206 1230 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.64 % Allowed : 15.47 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.77 (0.25), residues: 1128 helix: 2.67 (0.25), residues: 409 sheet: 1.15 (0.31), residues: 291 loop : -0.31 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 322 TYR 0.017 0.002 TYR S 103 PHE 0.019 0.002 PHE B 151 TRP 0.020 0.002 TRP B 82 HIS 0.008 0.002 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 ( 8593) covalent geometry : angle 0.65482 / 0.36 (11734) SS BOND : bond 0.01664 / 0.81 ( 3) SS BOND : angle 1.74326 / 0.93 ( 6) hydrogen bonds : bond 0.05957 / 4.11 ( 477) hydrogen bonds : angle 4.84008 / 3.33 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 ASN cc_start: 0.4862 (OUTLIER) cc_final: 0.4501 (t0) REVERT: R 153 TYR cc_start: 0.7291 (m-80) cc_final: 0.6879 (m-80) REVERT: R 303 ARG cc_start: 0.6693 (mmt90) cc_final: 0.6349 (mtm-85) REVERT: R 306 ARG cc_start: 0.6190 (mtt-85) cc_final: 0.5772 (mtp85) REVERT: R 323 ARG cc_start: 0.5529 (mtt180) cc_final: 0.5318 (mtm-85) REVERT: R 353 PHE cc_start: 0.6277 (t80) cc_final: 0.5956 (t80) REVERT: A 354 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.6393 (t80) outliers start: 21 outliers final: 9 residues processed: 152 average time/residue: 0.5284 time to fit residues: 85.7858 Evaluate side-chains 144 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ASN Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 253 SER Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [14, 70, 43, 0, 38, 16, 15, 72, 21, 103, 49] chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 ASN A 22 ASN A 256 ASN A 331 ASN S 3 GLN S 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.185829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122745 restraints weight = 8217.620| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.11 r_work: 0.3206 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8596 Z= 0.124 Angle : 0.515 6.947 11740 Z= 0.284 Chirality : 0.042 0.135 1385 Planarity : 0.003 0.040 1484 Dihedral : 4.260 19.536 1230 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.38 % Allowed : 16.73 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.92 (0.26), residues: 1128 helix: 2.94 (0.25), residues: 410 sheet: 1.19 (0.31), residues: 283 loop : -0.31 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 322 TYR 0.015 0.001 TYR S 178 PHE 0.015 0.001 PHE R 353 TRP 0.021 0.002 TRP B 82 HIS 0.006 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 8593) covalent geometry : angle 0.51405 / 0.28 (11734) SS BOND : bond 0.00981 / 0.48 ( 3) SS BOND : angle 1.33619 / 0.71 ( 6) hydrogen bonds : bond 0.04600 / 3.15 ( 477) hydrogen bonds : angle 4.51432 / 3.09 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: B 22 ARG cc_start: 0.7301 (mtt180) cc_final: 0.6990 (mtt180) REVERT: R 70 TYR cc_start: 0.5296 (m-80) cc_final: 0.5085 (m-80) REVERT: R 153 TYR cc_start: 0.7256 (m-80) cc_final: 0.6797 (m-80) REVERT: R 306 ARG cc_start: 0.6265 (mtt-85) cc_final: 0.5782 (mtp180) REVERT: R 353 PHE cc_start: 0.6330 (t80) cc_final: 0.5880 (t80) REVERT: A 354 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.6264 (t80) outliers start: 11 outliers final: 4 residues processed: 133 average time/residue: 0.5227 time to fit residues: 74.1637 Evaluate side-chains 129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 253 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [78, 62, 85, 11, 94, 99, 93, 10, 106, 35, 81] chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN C 59 ASN R 131 HIS A 22 ASN A 256 ASN A 331 ASN S 3 GLN S 171 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.184194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119677 restraints weight = 8232.695| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.05 r_work: 0.3200 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8596 Z= 0.168 Angle : 0.588 9.479 11740 Z= 0.321 Chirality : 0.044 0.166 1385 Planarity : 0.004 0.041 1484 Dihedral : 4.522 20.984 1230 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.64 % Allowed : 16.73 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.85 (0.25), residues: 1128 helix: 2.83 (0.24), residues: 409 sheet: 1.17 (0.31), residues: 289 loop : -0.32 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 322 TYR 0.014 0.002 TYR S 178 PHE 0.018 0.002 PHE B 151 TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 8593) covalent geometry : angle 0.58586 / 0.32 (11734) SS BOND : bond 0.01340 / 0.65 ( 3) SS BOND : angle 2.18809 / 1.22 ( 6) hydrogen bonds : bond 0.05316 / 3.68 ( 477) hydrogen bonds : angle 4.73584 / 3.25 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.341 Fit side-chains REVERT: R 153 TYR cc_start: 0.7216 (m-80) cc_final: 0.6851 (m-80) REVERT: R 224 CYS cc_start: 0.5141 (OUTLIER) cc_final: 0.4849 (t) REVERT: R 303 ARG cc_start: 0.6700 (mmt90) cc_final: 0.6394 (mtm180) REVERT: R 306 ARG cc_start: 0.6180 (mtt-85) cc_final: 0.5704 (mtp180) REVERT: R 353 PHE cc_start: 0.6435 (t80) cc_final: 0.5971 (t80) REVERT: A 247 MET cc_start: 0.8324 (mtm) cc_final: 0.7873 (mtt) REVERT: A 354 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.6332 (t80) outliers start: 13 outliers final: 7 residues processed: 134 average time/residue: 0.5475 time to fit residues: 78.1593 Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 253 SER Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [34, 67, 9, 88, 92, 13, 48, 32, 110, 72, 12] chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 ASN A 22 ASN A 256 ASN A 331 ASN S 3 GLN S 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.185675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123285 restraints weight = 8149.419| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.01 r_work: 0.3203 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8596 Z= 0.125 Angle : 0.529 7.288 11740 Z= 0.288 Chirality : 0.042 0.142 1385 Planarity : 0.003 0.040 1484 Dihedral : 4.265 19.638 1230 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.51 % Allowed : 16.98 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.93 (0.26), residues: 1128 helix: 2.97 (0.25), residues: 409 sheet: 1.20 (0.31), residues: 281 loop : -0.33 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 322 TYR 0.015 0.001 TYR S 178 PHE 0.015 0.001 PHE B 151 TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 8593) covalent geometry : angle 0.52732 / 0.29 (11734) SS BOND : bond 0.01032 / 0.50 ( 3) SS BOND : angle 1.75801 / 0.98 ( 6) hydrogen bonds : bond 0.04564 / 3.14 ( 477) hydrogen bonds : angle 4.54009 / 3.11 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: B 22 ARG cc_start: 0.7276 (mtt180) cc_final: 0.6968 (mtt180) REVERT: R 153 TYR cc_start: 0.7213 (m-80) cc_final: 0.6982 (m-80) REVERT: R 224 CYS cc_start: 0.5029 (OUTLIER) cc_final: 0.4744 (t) REVERT: R 306 ARG cc_start: 0.6223 (mtt-85) cc_final: 0.5759 (mtp180) REVERT: R 353 PHE cc_start: 0.6419 (t80) cc_final: 0.5973 (OUTLIER) REVERT: A 354 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.6258 (t80) outliers start: 12 outliers final: 7 residues processed: 132 average time/residue: 0.5152 time to fit residues: 72.6545 Evaluate side-chains 130 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 253 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [6, 49, 56, 61, 100, 48, 74, 99, 0, 43, 78] chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 99 optimal weight: 0.4980 chunk 0 optimal weight: 50.0000 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN C 59 ASN A 22 ASN A 256 ASN A 331 ASN S 3 GLN S 171 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.184914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.122841 restraints weight = 8198.826| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.90 r_work: 0.3208 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8596 Z= 0.144 Angle : 0.555 7.906 11740 Z= 0.303 Chirality : 0.043 0.154 1385 Planarity : 0.004 0.041 1484 Dihedral : 4.392 20.435 1230 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.51 % Allowed : 17.23 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.88 (0.25), residues: 1128 helix: 2.89 (0.25), residues: 409 sheet: 1.20 (0.31), residues: 283 loop : -0.35 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 322 TYR 0.015 0.001 TYR S 178 PHE 0.016 0.001 PHE B 151 TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8593) covalent geometry : angle 0.55348 / 0.30 (11734) SS BOND : bond 0.01165 / 0.57 ( 3) SS BOND : angle 1.69506 / 0.94 ( 6) hydrogen bonds : bond 0.04915 / 3.39 ( 477) hydrogen bonds : angle 4.62674 / 3.17 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.232 Fit side-chains REVERT: R 120 MET cc_start: 0.6490 (tpp) cc_final: 0.6218 (tpp) REVERT: R 153 TYR cc_start: 0.7091 (m-80) cc_final: 0.6821 (m-80) REVERT: R 224 CYS cc_start: 0.4847 (OUTLIER) cc_final: 0.4515 (t) REVERT: R 303 ARG cc_start: 0.6699 (mmt90) cc_final: 0.6415 (mtm180) REVERT: R 306 ARG cc_start: 0.6126 (mtt-85) cc_final: 0.5664 (mtp180) REVERT: R 353 PHE cc_start: 0.6503 (t80) cc_final: 0.6020 (t80) REVERT: A 247 MET cc_start: 0.8310 (mtm) cc_final: 0.7872 (mtt) REVERT: A 354 TYR cc_start: 0.6745 (OUTLIER) cc_final: 0.6255 (t80) outliers start: 12 outliers final: 7 residues processed: 132 average time/residue: 0.5509 time to fit residues: 77.4313 Evaluate side-chains 130 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 253 SER Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [61, 92, 110, 64, 74, 11, 101, 102, 84, 41, 37] chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 37 optimal weight: 0.0370 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 ASN A 22 ASN A 256 ASN A 331 ASN S 3 GLN S 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.186799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124196 restraints weight = 8240.661| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.06 r_work: 0.3232 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8596 Z= 0.107 Angle : 0.490 6.322 11740 Z= 0.269 Chirality : 0.041 0.132 1385 Planarity : 0.003 0.040 1484 Dihedral : 4.078 18.977 1230 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.51 % Allowed : 17.11 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.02 (0.26), residues: 1128 helix: 3.06 (0.25), residues: 409 sheet: 1.21 (0.31), residues: 282 loop : -0.26 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 322 TYR 0.016 0.001 TYR S 178 PHE 0.013 0.001 PHE R 353 TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 ( 8593) covalent geometry : angle 0.48886 / 0.27 (11734) SS BOND : bond 0.00820 / 0.40 ( 3) SS BOND : angle 1.33657 / 0.73 ( 6) hydrogen bonds : bond 0.04114 / 2.83 ( 477) hydrogen bonds : angle 4.42471 / 3.03 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.298 Fit side-chains REVERT: B 46 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7939 (mpt90) REVERT: R 224 CYS cc_start: 0.4722 (OUTLIER) cc_final: 0.4226 (t) REVERT: R 306 ARG cc_start: 0.6220 (mtt-85) cc_final: 0.5729 (mtp180) REVERT: R 353 PHE cc_start: 0.6535 (t80) cc_final: 0.6079 (OUTLIER) REVERT: A 247 MET cc_start: 0.8258 (mtm) cc_final: 0.7820 (mtt) REVERT: A 354 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.6206 (t80) outliers start: 12 outliers final: 9 residues processed: 132 average time/residue: 0.5144 time to fit residues: 72.5002 Evaluate side-chains 131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 253 SER Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [73, 92, 18, 26, 82, 100, 67, 0, 90, 37, 27] chunk 73 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 0.0980 chunk 100 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 ASN A 22 ASN A 256 ASN A 331 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.184924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122029 restraints weight = 8193.188| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.14 r_work: 0.3200 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8596 Z= 0.149 Angle : 0.564 8.163 11740 Z= 0.307 Chirality : 0.043 0.154 1385 Planarity : 0.004 0.042 1484 Dihedral : 4.377 20.489 1230 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.51 % Allowed : 17.36 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.90 (0.26), residues: 1128 helix: 2.89 (0.25), residues: 409 sheet: 1.12 (0.31), residues: 291 loop : -0.28 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 206 TYR 0.017 0.002 TYR R 70 PHE 0.016 0.002 PHE B 151 TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 8593) covalent geometry : angle 0.56262 / 0.31 (11734) SS BOND : bond 0.01177 / 0.57 ( 3) SS BOND : angle 1.59718 / 0.88 ( 6) hydrogen bonds : bond 0.04918 / 3.40 ( 477) hydrogen bonds : angle 4.63044 / 3.18 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5440.13 seconds wall clock time: 92 minutes 45.52 seconds (5565.52 seconds total)