Starting phenix.real_space_refine on Fri Aug 22 17:40:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gea_29962/08_2025/8gea_29962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gea_29962/08_2025/8gea_29962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gea_29962/08_2025/8gea_29962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gea_29962/08_2025/8gea_29962.map" model { file = "/net/cci-nas-00/data/ceres_data/8gea_29962/08_2025/8gea_29962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gea_29962/08_2025/8gea_29962.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 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 42 5.16 5 C 4221 2.51 5 N 1140 2.21 5 O 1148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6551 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1751 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'GLU:plan': 18, 'ASP:plan': 12, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 184 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2392 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 7, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 10, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "G" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 335 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2058 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 9, 'TRP:plan': 1, 'GLN:plan1': 6, 'ASP:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 115 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.77, per 1000 atoms: 0.27 Number of scatterers: 6551 At special positions: 0 Unit cell: (68.9, 97.52, 128.26, 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 42 16.00 O 1148 8.00 N 1140 7.00 C 4221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 399.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 48.6% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.967A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.642A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.418A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.510A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 14 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.669A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.777A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.295A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 Proline residue: R 168 - end of helix removed outlier: 3.566A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.711A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.879A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 4.136A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.597A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.514A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.065A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 93 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.533A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.843A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.793A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.708A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.537A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1134 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: 0.84 Time building geometry restraints manager: 0.68 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: 2117 1.34 - 1.46: 1403 1.46 - 1.58: 3114 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6692 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.568 -0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.438 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.563 -0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.483 -0.032 2.00e-02 2.50e+03 2.59e+00 ... (remaining 6687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 8896 1.17 - 2.34: 195 2.34 - 3.51: 36 3.51 - 4.69: 9 4.69 - 5.86: 9 Bond angle restraints: 9145 Sorted by residual: angle pdb=" N GLY A 329 " pdb=" CA GLY A 329 " pdb=" C GLY A 329 " ideal model delta sigma weight residual 113.18 107.88 5.30 2.37e+00 1.78e-01 5.01e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.49 -5.86 3.00e+00 1.11e-01 3.81e+00 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.72 117.50 3.22 1.67e+00 3.59e-01 3.71e+00 angle pdb=" N ILE R 55 " pdb=" CA ILE R 55 " pdb=" CB ILE R 55 " ideal model delta sigma weight residual 110.54 112.95 -2.41 1.36e+00 5.41e-01 3.15e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 116.05 -5.16 3.00e+00 1.11e-01 2.96e+00 ... (remaining 9140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3566 17.97 - 35.94: 284 35.94 - 53.91: 23 53.91 - 71.87: 3 71.87 - 89.84: 4 Dihedral angle restraints: 3880 sinusoidal: 1249 harmonic: 2631 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CG ARG A 336 " pdb=" CD ARG A 336 " pdb=" NE ARG A 336 " pdb=" CZ ARG A 336 " ideal model delta sinusoidal sigma weight residual 90.00 133.08 -43.08 2 1.50e+01 4.44e-03 9.95e+00 dihedral pdb=" CA ALA R 85 " pdb=" C ALA R 85 " pdb=" N VAL R 86 " pdb=" CA VAL R 86 " ideal model delta harmonic sigma weight residual -180.00 -164.76 -15.24 0 5.00e+00 4.00e-02 9.29e+00 ... (remaining 3877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 704 0.030 - 0.061: 264 0.061 - 0.091: 74 0.091 - 0.121: 48 0.121 - 0.151: 5 Chirality restraints: 1095 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CB THR A 263 " pdb=" CA THR A 263 " pdb=" OG1 THR A 263 " pdb=" CG2 THR A 263 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 1092 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.010 2.00e-02 2.50e+03 1.05e-02 2.22e+00 pdb=" CG TYR B 59 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.017 5.00e-02 4.00e+02 2.53e-02 1.02e+00 pdb=" N PRO B 194 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.016 5.00e-02 4.00e+02 2.50e-02 9.96e-01 pdb=" N PRO B 236 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.014 5.00e-02 4.00e+02 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1600 2.80 - 3.32: 6354 3.32 - 3.85: 10867 3.85 - 4.37: 11896 4.37 - 4.90: 21791 Nonbonded interactions: 52508 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" O HIS G 44 " model vdw 2.269 3.040 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.299 3.120 nonbonded pdb=" OE1 GLU R 107 " pdb=" OH TYR R 174 " model vdw 2.313 3.040 nonbonded pdb=" NH1 ARG B 49 " pdb=" O PHE G 61 " model vdw 2.316 3.120 nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.327 3.040 ... (remaining 52503 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.160 Find NCS groups from input model: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 0.003 0.051 6693 Z= 0.148 Angle : 0.476 5.858 9147 Z= 0.255 Chirality : 0.039 0.151 1095 Planarity : 0.003 0.025 1150 Dihedral : 12.734 89.842 2169 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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 aren not related in a simple way. whole: 1.14 (0.28), residues: 888 helix: 2.33 (0.26), residues: 396 sheet: 0.02 (0.40), residues: 171 loop : -0.83 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.026 0.001 TYR B 59 PHE 0.010 0.001 PHE R 289 TRP 0.009 0.001 TRP A 281 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6692) covalent geometry : angle 0.47563 ( 9145) SS BOND : bond 0.00334 ( 1) SS BOND : angle 0.49710 ( 2) hydrogen bonds : bond 0.15376 ( 390) hydrogen bonds : angle 6.20970 ( 1134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.153 Fit side-chains REVERT: R 277 ILE cc_start: 0.7992 (tt) cc_final: 0.7757 (tp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0699 time to fit residues: 8.3197 Evaluate side-chains 68 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0010 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.122376 restraints weight = 10290.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125512 restraints weight = 6317.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127725 restraints weight = 4553.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.129177 restraints weight = 3610.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129948 restraints weight = 3063.040| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6693 Z= 0.132 Angle : 0.468 5.265 9147 Z= 0.261 Chirality : 0.040 0.179 1095 Planarity : 0.003 0.027 1150 Dihedral : 3.881 30.490 976 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.67 % Allowed : 8.53 % Favored : 89.80 % 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 aren not related in a simple way. whole: 1.28 (0.28), residues: 888 helix: 2.46 (0.26), residues: 400 sheet: 0.04 (0.40), residues: 173 loop : -0.80 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.018 0.001 TYR B 59 PHE 0.014 0.001 PHE R 289 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6692) covalent geometry : angle 0.46789 ( 9145) SS BOND : bond 0.00317 ( 1) SS BOND : angle 0.36043 ( 2) hydrogen bonds : bond 0.04000 ( 390) hydrogen bonds : angle 4.56703 ( 1134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.252 Fit side-chains REVERT: R 36 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6708 (ttp) REVERT: R 58 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7872 (mp) REVERT: R 277 ILE cc_start: 0.7939 (tt) cc_final: 0.7707 (tp) outliers start: 10 outliers final: 6 residues processed: 82 average time/residue: 0.0658 time to fit residues: 7.7697 Evaluate side-chains 77 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 159 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 74 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118014 restraints weight = 9773.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121308 restraints weight = 5731.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.123651 restraints weight = 4024.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125208 restraints weight = 3122.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.126134 restraints weight = 2608.046| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6693 Z= 0.147 Angle : 0.464 5.399 9147 Z= 0.256 Chirality : 0.040 0.194 1095 Planarity : 0.003 0.027 1150 Dihedral : 3.849 30.287 976 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.01 % Allowed : 11.87 % Favored : 86.12 % 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 aren not related in a simple way. whole: 1.32 (0.28), residues: 888 helix: 2.47 (0.26), residues: 400 sheet: 0.03 (0.39), residues: 171 loop : -0.72 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.020 0.001 TYR B 59 PHE 0.017 0.001 PHE B 199 TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6692) covalent geometry : angle 0.46365 ( 9145) SS BOND : bond 0.00459 ( 1) SS BOND : angle 0.44920 ( 2) hydrogen bonds : bond 0.03924 ( 390) hydrogen bonds : angle 4.33645 ( 1134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.173 Fit side-chains REVERT: R 36 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6798 (ttp) REVERT: R 58 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7934 (mp) REVERT: R 277 ILE cc_start: 0.7968 (tt) cc_final: 0.7719 (tp) outliers start: 12 outliers final: 8 residues processed: 80 average time/residue: 0.0630 time to fit residues: 7.3966 Evaluate side-chains 82 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** 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 = 0.3753 r_free = 0.3753 target = 0.138004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117185 restraints weight = 10280.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120577 restraints weight = 5959.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122906 restraints weight = 4140.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124524 restraints weight = 3214.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125693 restraints weight = 2681.321| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6693 Z= 0.168 Angle : 0.478 5.496 9147 Z= 0.263 Chirality : 0.040 0.152 1095 Planarity : 0.003 0.026 1150 Dihedral : 3.926 31.083 976 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.17 % Allowed : 14.21 % Favored : 83.61 % 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 aren not related in a simple way. whole: 1.19 (0.28), residues: 888 helix: 2.35 (0.26), residues: 399 sheet: -0.12 (0.39), residues: 170 loop : -0.69 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.024 0.001 TYR B 59 PHE 0.020 0.001 PHE B 199 TRP 0.009 0.001 TRP B 169 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6692) covalent geometry : angle 0.47768 ( 9145) SS BOND : bond 0.00581 ( 1) SS BOND : angle 0.60617 ( 2) hydrogen bonds : bond 0.03917 ( 390) hydrogen bonds : angle 4.27836 ( 1134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.260 Fit side-chains REVERT: R 58 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8013 (mp) outliers start: 13 outliers final: 12 residues processed: 84 average time/residue: 0.0643 time to fit residues: 7.9647 Evaluate side-chains 80 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 0.0040 chunk 47 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** 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 = 0.3781 r_free = 0.3781 target = 0.140468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119587 restraints weight = 10234.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123011 restraints weight = 5914.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125190 restraints weight = 4098.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126992 restraints weight = 3201.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128008 restraints weight = 2642.468| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6693 Z= 0.113 Angle : 0.445 6.719 9147 Z= 0.243 Chirality : 0.040 0.215 1095 Planarity : 0.003 0.027 1150 Dihedral : 3.806 31.496 976 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.01 % Allowed : 14.05 % Favored : 83.95 % 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 aren not related in a simple way. whole: 1.27 (0.29), residues: 888 helix: 2.41 (0.26), residues: 406 sheet: -0.16 (0.38), residues: 170 loop : -0.68 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.013 0.001 TYR B 59 PHE 0.013 0.001 PHE R 289 TRP 0.008 0.001 TRP B 169 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6692) covalent geometry : angle 0.44467 ( 9145) SS BOND : bond 0.00338 ( 1) SS BOND : angle 0.43109 ( 2) hydrogen bonds : bond 0.03577 ( 390) hydrogen bonds : angle 4.08125 ( 1134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.252 Fit side-chains REVERT: R 36 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6826 (ttp) REVERT: R 58 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7983 (mp) outliers start: 12 outliers final: 7 residues processed: 85 average time/residue: 0.0555 time to fit residues: 7.0984 Evaluate side-chains 78 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 84 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 39 optimal weight: 0.1980 chunk 73 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** 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 = 0.3799 r_free = 0.3799 target = 0.140992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121159 restraints weight = 10101.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124307 restraints weight = 6056.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126502 restraints weight = 4313.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128061 restraints weight = 3386.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129060 restraints weight = 2832.619| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6693 Z= 0.104 Angle : 0.434 6.432 9147 Z= 0.237 Chirality : 0.039 0.177 1095 Planarity : 0.003 0.027 1150 Dihedral : 3.735 31.826 976 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.68 % Allowed : 14.55 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.29), residues: 888 helix: 2.46 (0.26), residues: 406 sheet: -0.10 (0.38), residues: 169 loop : -0.65 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.012 0.001 TYR R 199 PHE 0.012 0.001 PHE R 289 TRP 0.008 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 6692) covalent geometry : angle 0.43431 ( 9145) SS BOND : bond 0.00297 ( 1) SS BOND : angle 0.34417 ( 2) hydrogen bonds : bond 0.03429 ( 390) hydrogen bonds : angle 3.96689 ( 1134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.249 Fit side-chains REVERT: B 59 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7342 (m-80) REVERT: B 211 TRP cc_start: 0.9029 (m100) cc_final: 0.8640 (m100) REVERT: R 36 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6893 (ttp) REVERT: R 58 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7969 (mp) REVERT: R 277 ILE cc_start: 0.7745 (tt) cc_final: 0.7535 (tp) outliers start: 16 outliers final: 10 residues processed: 88 average time/residue: 0.0609 time to fit residues: 7.7037 Evaluate side-chains 85 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 71 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 0.2980 chunk 65 optimal weight: 5.9990 chunk 26 optimal weight: 0.0270 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 overall best weight: 0.2638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** 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 = 0.3821 r_free = 0.3821 target = 0.142916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123239 restraints weight = 10027.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126524 restraints weight = 5986.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128754 restraints weight = 4203.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.130082 restraints weight = 3283.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131264 restraints weight = 2774.779| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6693 Z= 0.090 Angle : 0.419 6.323 9147 Z= 0.229 Chirality : 0.039 0.218 1095 Planarity : 0.003 0.028 1150 Dihedral : 3.615 31.720 976 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.34 % Allowed : 15.72 % Favored : 81.94 % 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 aren not related in a simple way. whole: 1.44 (0.29), residues: 888 helix: 2.56 (0.26), residues: 405 sheet: -0.01 (0.38), residues: 169 loop : -0.64 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.011 0.001 TYR R 199 PHE 0.011 0.001 PHE R 289 TRP 0.009 0.001 TRP R 313 HIS 0.002 0.000 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 6692) covalent geometry : angle 0.41891 ( 9145) SS BOND : bond 0.00147 ( 1) SS BOND : angle 0.18562 ( 2) hydrogen bonds : bond 0.03219 ( 390) hydrogen bonds : angle 3.83061 ( 1134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.274 Fit side-chains REVERT: A 236 GLN cc_start: 0.8637 (pt0) cc_final: 0.8382 (pt0) REVERT: B 58 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8380 (mp) REVERT: B 59 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.7250 (m-80) REVERT: B 211 TRP cc_start: 0.8933 (m100) cc_final: 0.8646 (m100) REVERT: B 273 ILE cc_start: 0.8755 (mp) cc_final: 0.8483 (mp) REVERT: R 36 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7019 (ttp) REVERT: R 58 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8017 (mp) REVERT: R 277 ILE cc_start: 0.7839 (tt) cc_final: 0.7578 (tp) outliers start: 14 outliers final: 9 residues processed: 87 average time/residue: 0.0597 time to fit residues: 7.7341 Evaluate side-chains 87 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** 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 = 0.3772 r_free = 0.3772 target = 0.139602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118814 restraints weight = 10238.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122225 restraints weight = 5948.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124573 restraints weight = 4125.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126110 restraints weight = 3194.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126950 restraints weight = 2670.469| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6693 Z= 0.149 Angle : 0.474 6.134 9147 Z= 0.260 Chirality : 0.040 0.220 1095 Planarity : 0.003 0.026 1150 Dihedral : 3.770 32.897 976 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.51 % Allowed : 16.72 % Favored : 80.77 % 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 aren not related in a simple way. whole: 1.30 (0.29), residues: 888 helix: 2.48 (0.26), residues: 400 sheet: -0.18 (0.39), residues: 170 loop : -0.64 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.015 0.001 TYR B 59 PHE 0.019 0.001 PHE B 199 TRP 0.009 0.001 TRP B 63 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6692) covalent geometry : angle 0.47378 ( 9145) SS BOND : bond 0.00569 ( 1) SS BOND : angle 0.60078 ( 2) hydrogen bonds : bond 0.03624 ( 390) hydrogen bonds : angle 3.99194 ( 1134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.289 Fit side-chains REVERT: A 236 GLN cc_start: 0.8676 (pt0) cc_final: 0.8444 (pt0) REVERT: B 59 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: B 169 TRP cc_start: 0.9176 (m100) cc_final: 0.8825 (m100) REVERT: B 211 TRP cc_start: 0.9075 (m100) cc_final: 0.8691 (m100) REVERT: B 273 ILE cc_start: 0.8798 (mp) cc_final: 0.8563 (mp) REVERT: R 36 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6817 (ttp) REVERT: R 58 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7948 (mp) outliers start: 15 outliers final: 11 residues processed: 82 average time/residue: 0.0647 time to fit residues: 7.9005 Evaluate side-chains 85 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.139288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119398 restraints weight = 10158.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122523 restraints weight = 6071.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124530 restraints weight = 4312.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126212 restraints weight = 3424.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127208 restraints weight = 2853.560| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6693 Z= 0.130 Angle : 0.461 5.662 9147 Z= 0.252 Chirality : 0.040 0.212 1095 Planarity : 0.003 0.027 1150 Dihedral : 3.789 33.832 976 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.34 % Allowed : 17.39 % Favored : 80.27 % 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 aren not related in a simple way. whole: 1.24 (0.29), residues: 888 helix: 2.44 (0.26), residues: 401 sheet: -0.27 (0.38), residues: 175 loop : -0.66 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.012 0.001 TYR B 59 PHE 0.015 0.001 PHE B 199 TRP 0.008 0.001 TRP B 297 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6692) covalent geometry : angle 0.46073 ( 9145) SS BOND : bond 0.00410 ( 1) SS BOND : angle 0.47087 ( 2) hydrogen bonds : bond 0.03517 ( 390) hydrogen bonds : angle 3.97639 ( 1134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.266 Fit side-chains REVERT: B 59 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: B 211 TRP cc_start: 0.9082 (m100) cc_final: 0.8694 (m100) REVERT: R 36 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6879 (ttp) REVERT: R 58 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7981 (mp) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 0.0634 time to fit residues: 7.7748 Evaluate side-chains 84 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 0.0050 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.138762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.117987 restraints weight = 10161.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121345 restraints weight = 5915.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123682 restraints weight = 4127.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125140 restraints weight = 3196.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126278 restraints weight = 2685.337| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6693 Z= 0.152 Angle : 0.474 5.683 9147 Z= 0.260 Chirality : 0.040 0.208 1095 Planarity : 0.003 0.026 1150 Dihedral : 3.871 34.552 976 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.84 % Allowed : 16.89 % Favored : 80.27 % 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 aren not related in a simple way. whole: 1.15 (0.29), residues: 888 helix: 2.37 (0.26), residues: 401 sheet: -0.33 (0.38), residues: 175 loop : -0.69 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.014 0.001 TYR B 59 PHE 0.018 0.001 PHE B 199 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6692) covalent geometry : angle 0.47377 ( 9145) SS BOND : bond 0.00531 ( 1) SS BOND : angle 0.59521 ( 2) hydrogen bonds : bond 0.03667 ( 390) hydrogen bonds : angle 4.04761 ( 1134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.249 Fit side-chains REVERT: B 59 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: B 211 TRP cc_start: 0.9106 (m100) cc_final: 0.8706 (m100) REVERT: R 36 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6779 (ttp) REVERT: R 58 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7984 (mp) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.0616 time to fit residues: 7.4678 Evaluate side-chains 87 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.139201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118394 restraints weight = 10174.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121771 restraints weight = 5913.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.124130 restraints weight = 4119.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125647 restraints weight = 3189.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.126850 restraints weight = 2666.641| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6693 Z= 0.138 Angle : 0.464 5.582 9147 Z= 0.256 Chirality : 0.040 0.204 1095 Planarity : 0.003 0.027 1150 Dihedral : 3.866 34.540 976 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.68 % Allowed : 17.06 % Favored : 80.27 % 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 aren not related in a simple way. whole: 1.17 (0.29), residues: 888 helix: 2.40 (0.26), residues: 400 sheet: -0.39 (0.38), residues: 175 loop : -0.64 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.013 0.001 TYR B 59 PHE 0.017 0.001 PHE B 199 TRP 0.008 0.001 TRP B 297 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6692) covalent geometry : angle 0.46443 ( 9145) SS BOND : bond 0.00448 ( 1) SS BOND : angle 0.52395 ( 2) hydrogen bonds : bond 0.03606 ( 390) hydrogen bonds : angle 4.01926 ( 1134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1111.43 seconds wall clock time: 19 minutes 52.01 seconds (1192.01 seconds total)