Starting phenix.real_space_refine on Sat Aug 23 00:26:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8flr_29284/08_2025/8flr_29284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flr_29284/08_2025/8flr_29284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8flr_29284/08_2025/8flr_29284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flr_29284/08_2025/8flr_29284.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8flr_29284/08_2025/8flr_29284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flr_29284/08_2025/8flr_29284.map" } resolution = 2.94 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= -0.002 sd= 0.112 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 56 5.16 5 C 5688 2.51 5 N 1552 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 8928 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1897 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2563 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 403 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 957 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 272 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2826 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 3 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 8, 'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 1.85, per 1000 atoms: 0.21 Number of scatterers: 8928 At special positions: 0 Unit cell: (73.1, 94.35, 173.4, 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 1632 8.00 N 1552 7.00 C 5688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 392.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 43.2% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.542A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.535A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.757A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.492A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.639A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.590A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.537A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 54 Processing helix chain 'R' and resid 177 through 212 removed outlier: 4.336A pdb=" N ARG R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.660A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY R 303 " --> pdb=" O ILE R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.676A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 356 through 359 removed outlier: 3.987A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 removed outlier: 3.524A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.293A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 479 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.811A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.758A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.520A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.151A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.608A 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: 3.984A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.937A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.535A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.670A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.529A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 removed outlier: 3.705A pdb=" N GLU R 111 " --> pdb=" O TRP R 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 499 hydrogen bonds defined for protein. 1440 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: 1.66 Time building geometry restraints manager: 0.83 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: 2905 1.34 - 1.46: 2048 1.46 - 1.58: 4089 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 9120 Sorted by residual: bond pdb=" N LEU R 321 " pdb=" CA LEU R 321 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.23e-02 6.61e+03 8.29e+00 bond pdb=" N VAL R 432 " pdb=" CA VAL R 432 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.03e+00 bond pdb=" N VAL R 171 " pdb=" CA VAL R 171 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.72e+00 bond pdb=" N ILE P 28 " pdb=" CA ILE P 28 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.36e+00 bond pdb=" N GLU R 317 " pdb=" CA GLU R 317 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.28e-02 6.10e+03 7.20e+00 ... (remaining 9115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 12143 1.96 - 3.91: 211 3.91 - 5.87: 22 5.87 - 7.82: 2 7.82 - 9.78: 1 Bond angle restraints: 12379 Sorted by residual: angle pdb=" CA CYS R 217 " pdb=" C CYS R 217 " pdb=" O CYS R 217 " ideal model delta sigma weight residual 121.40 116.94 4.46 1.13e+00 7.83e-01 1.56e+01 angle pdb=" N ILE P 31 " pdb=" CA ILE P 31 " pdb=" C ILE P 31 " ideal model delta sigma weight residual 112.80 108.57 4.23 1.15e+00 7.56e-01 1.35e+01 angle pdb=" C VAL R 334 " pdb=" N PHE R 335 " pdb=" CA PHE R 335 " ideal model delta sigma weight residual 121.14 114.94 6.20 1.75e+00 3.27e-01 1.25e+01 angle pdb=" CA TYR R 191 " pdb=" CB TYR R 191 " pdb=" CG TYR R 191 " ideal model delta sigma weight residual 113.90 119.99 -6.09 1.80e+00 3.09e-01 1.15e+01 angle pdb=" CA ARG R 219 " pdb=" C ARG R 219 " pdb=" O ARG R 219 " ideal model delta sigma weight residual 120.82 117.50 3.32 1.05e+00 9.07e-01 9.99e+00 ... (remaining 12374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4893 17.93 - 35.86: 365 35.86 - 53.79: 75 53.79 - 71.72: 14 71.72 - 89.65: 9 Dihedral angle restraints: 5356 sinusoidal: 2023 harmonic: 3333 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 136.17 -43.17 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 5353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1092 0.049 - 0.099: 235 0.099 - 0.148: 52 0.148 - 0.198: 7 0.198 - 0.247: 1 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA CYS R 217 " pdb=" N CYS R 217 " pdb=" C CYS R 217 " pdb=" CB CYS R 217 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE P 31 " pdb=" N ILE P 31 " pdb=" C ILE P 31 " pdb=" CB ILE P 31 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA PHE R 335 " pdb=" N PHE R 335 " pdb=" C PHE R 335 " pdb=" CB PHE R 335 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 1384 not shown) Planarity restraints: 1575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS R 216 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C HIS R 216 " 0.039 2.00e-02 2.50e+03 pdb=" O HIS R 216 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS R 217 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 376 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ILE R 376 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE R 376 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU R 377 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 236 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 ... (remaining 1572 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 701 2.74 - 3.28: 8964 3.28 - 3.82: 15715 3.82 - 4.36: 19096 4.36 - 4.90: 32751 Nonbonded interactions: 77227 Sorted by model distance: nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.201 3.040 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.207 3.120 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.216 3.040 nonbonded pdb=" O ALA R 242 " pdb=" OG SER R 246 " model vdw 2.218 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.221 3.040 ... (remaining 77222 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.070 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: 0.000 Load rotamer database and sin/cos tables:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 0.037 9126 Z= 0.213 Angle : 0.591 9.776 12391 Z= 0.365 Chirality : 0.044 0.247 1387 Planarity : 0.004 0.042 1575 Dihedral : 13.800 89.652 3184 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.11 % Allowed : 0.65 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.25), residues: 1125 helix: 2.06 (0.25), residues: 442 sheet: -0.27 (0.32), residues: 226 loop : 0.28 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.020 0.001 TYR N 60 PHE 0.012 0.001 PHE A 212 TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9120) covalent geometry : angle 0.58900 (12379) SS BOND : bond 0.00126 ( 6) SS BOND : angle 1.50256 ( 12) hydrogen bonds : bond 0.13207 ( 499) hydrogen bonds : angle 5.91908 ( 1440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 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: 1 poor density : 139 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6587 (p0) cc_final: 0.6264 (p0) REVERT: B 153 ASP cc_start: 0.7840 (p0) cc_final: 0.7570 (p0) REVERT: R 189 MET cc_start: 0.7184 (tmm) cc_final: 0.6881 (tmt) REVERT: R 390 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.7294 (ttm170) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.5502 time to fit residues: 82.2632 Evaluate side-chains 112 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.0470 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 125 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.198472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.154566 restraints weight = 9050.921| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.78 r_work: 0.3496 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9126 Z= 0.217 Angle : 0.613 14.724 12391 Z= 0.324 Chirality : 0.044 0.185 1387 Planarity : 0.004 0.051 1575 Dihedral : 4.634 24.894 1244 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.85 % Allowed : 6.64 % Favored : 91.50 % 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: 1.36 (0.25), residues: 1125 helix: 2.43 (0.24), residues: 434 sheet: -0.20 (0.32), residues: 212 loop : 0.07 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.037 0.002 TYR R 191 PHE 0.035 0.002 PHE R 335 TRP 0.017 0.002 TRP R 298 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9120) covalent geometry : angle 0.61011 (12379) SS BOND : bond 0.00240 ( 6) SS BOND : angle 2.05812 ( 12) hydrogen bonds : bond 0.05006 ( 499) hydrogen bonds : angle 4.93560 ( 1440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 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: 17 poor density : 120 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7374 (p0) cc_final: 0.6922 (p0) REVERT: B 134 ARG cc_start: 0.6931 (ptm160) cc_final: 0.6307 (ptm160) REVERT: P 11 LYS cc_start: 0.8051 (tttm) cc_final: 0.7508 (ttmt) REVERT: R 214 ARG cc_start: 0.7509 (ptm160) cc_final: 0.7124 (pmm150) REVERT: R 390 ARG cc_start: 0.7945 (ttp-110) cc_final: 0.7597 (ttm170) REVERT: R 411 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7836 (mp) outliers start: 17 outliers final: 11 residues processed: 128 average time/residue: 0.5966 time to fit residues: 81.4530 Evaluate side-chains 118 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 15 optimal weight: 0.0370 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.203895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.162153 restraints weight = 9005.450| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.74 r_work: 0.3559 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9126 Z= 0.118 Angle : 0.510 12.535 12391 Z= 0.271 Chirality : 0.040 0.163 1387 Planarity : 0.004 0.048 1575 Dihedral : 4.277 22.839 1244 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.85 % Allowed : 9.59 % Favored : 88.56 % 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: 1.60 (0.25), residues: 1125 helix: 2.74 (0.24), residues: 435 sheet: -0.25 (0.32), residues: 212 loop : 0.17 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.029 0.001 TYR R 191 PHE 0.030 0.001 PHE R 335 TRP 0.014 0.001 TRP R 298 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9120) covalent geometry : angle 0.50860 (12379) SS BOND : bond 0.00189 ( 6) SS BOND : angle 1.19981 ( 12) hydrogen bonds : bond 0.04097 ( 499) hydrogen bonds : angle 4.61506 ( 1440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 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: 17 poor density : 123 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7386 (p0) cc_final: 0.6905 (p0) REVERT: B 155 ASN cc_start: 0.7840 (t0) cc_final: 0.7591 (m-40) REVERT: N 29 PHE cc_start: 0.7352 (t80) cc_final: 0.7081 (t80) REVERT: R 214 ARG cc_start: 0.7471 (ptm160) cc_final: 0.7098 (pmm150) REVERT: R 317 GLU cc_start: 0.4924 (tt0) cc_final: 0.4707 (tt0) REVERT: R 379 ILE cc_start: 0.7346 (pt) cc_final: 0.7122 (pt) REVERT: R 390 ARG cc_start: 0.7969 (ttp-110) cc_final: 0.7606 (ttm170) outliers start: 17 outliers final: 7 residues processed: 129 average time/residue: 0.5867 time to fit residues: 80.8064 Evaluate side-chains 118 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.0070 chunk 91 optimal weight: 0.6980 chunk 80 optimal weight: 0.0670 chunk 58 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.205888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.164610 restraints weight = 9111.368| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.65 r_work: 0.3595 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9126 Z= 0.106 Angle : 0.487 10.931 12391 Z= 0.260 Chirality : 0.040 0.168 1387 Planarity : 0.004 0.050 1575 Dihedral : 4.076 21.420 1244 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.07 % Allowed : 11.55 % Favored : 86.38 % 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: 1.78 (0.26), residues: 1125 helix: 2.90 (0.24), residues: 437 sheet: -0.14 (0.33), residues: 213 loop : 0.24 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.027 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.012 0.001 TRP R 298 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9120) covalent geometry : angle 0.48623 (12379) SS BOND : bond 0.00170 ( 6) SS BOND : angle 1.14644 ( 12) hydrogen bonds : bond 0.03835 ( 499) hydrogen bonds : angle 4.44692 ( 1440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7412 (p0) cc_final: 0.6925 (p0) REVERT: B 155 ASN cc_start: 0.7750 (t0) cc_final: 0.7521 (m-40) REVERT: N 29 PHE cc_start: 0.7309 (t80) cc_final: 0.7067 (t80) REVERT: R 214 ARG cc_start: 0.7444 (ptm160) cc_final: 0.7059 (pmm150) REVERT: R 390 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7562 (ttm170) outliers start: 19 outliers final: 11 residues processed: 135 average time/residue: 0.5310 time to fit residues: 77.0351 Evaluate side-chains 124 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.0870 chunk 55 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 0.0050 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.206248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163704 restraints weight = 9090.078| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.70 r_work: 0.3605 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9126 Z= 0.106 Angle : 0.487 10.349 12391 Z= 0.259 Chirality : 0.040 0.207 1387 Planarity : 0.004 0.051 1575 Dihedral : 4.056 25.614 1244 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.07 % Allowed : 12.09 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.26), residues: 1125 helix: 2.83 (0.24), residues: 443 sheet: -0.15 (0.32), residues: 217 loop : 0.22 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 197 TYR 0.023 0.001 TYR R 191 PHE 0.016 0.001 PHE R 335 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9120) covalent geometry : angle 0.48570 (12379) SS BOND : bond 0.00156 ( 6) SS BOND : angle 1.04245 ( 12) hydrogen bonds : bond 0.03780 ( 499) hydrogen bonds : angle 4.38893 ( 1440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7402 (mtt90) REVERT: A 240 ASP cc_start: 0.7344 (p0) cc_final: 0.6872 (p0) REVERT: B 134 ARG cc_start: 0.6742 (ptm160) cc_final: 0.6228 (ptm160) REVERT: B 155 ASN cc_start: 0.7622 (t0) cc_final: 0.7402 (m-40) REVERT: N 29 PHE cc_start: 0.7338 (t80) cc_final: 0.7058 (t80) REVERT: R 214 ARG cc_start: 0.7385 (ptm160) cc_final: 0.7056 (pmm150) REVERT: R 390 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7562 (ttm170) outliers start: 19 outliers final: 8 residues processed: 127 average time/residue: 0.5110 time to fit residues: 69.8181 Evaluate side-chains 120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 8.9990 chunk 83 optimal weight: 50.0000 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.203000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.159968 restraints weight = 9038.623| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.11 r_work: 0.3521 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9126 Z= 0.144 Angle : 0.533 12.383 12391 Z= 0.280 Chirality : 0.041 0.176 1387 Planarity : 0.004 0.053 1575 Dihedral : 4.218 24.540 1244 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.18 % Allowed : 12.96 % Favored : 84.86 % 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: 1.67 (0.26), residues: 1125 helix: 2.75 (0.24), residues: 443 sheet: -0.26 (0.32), residues: 231 loop : 0.29 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 197 TYR 0.026 0.001 TYR R 191 PHE 0.035 0.001 PHE R 335 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9120) covalent geometry : angle 0.53092 (12379) SS BOND : bond 0.00168 ( 6) SS BOND : angle 1.45731 ( 12) hydrogen bonds : bond 0.04046 ( 499) hydrogen bonds : angle 4.47473 ( 1440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7159 (p0) cc_final: 0.6681 (p0) REVERT: B 134 ARG cc_start: 0.6767 (ptm160) cc_final: 0.6278 (ptm160) REVERT: B 155 ASN cc_start: 0.7726 (t0) cc_final: 0.7456 (m-40) REVERT: B 220 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: N 29 PHE cc_start: 0.7380 (t80) cc_final: 0.7124 (t80) REVERT: R 214 ARG cc_start: 0.7301 (ptm160) cc_final: 0.6962 (pmm150) REVERT: R 390 ARG cc_start: 0.8001 (ttp-110) cc_final: 0.7498 (ttm170) REVERT: R 391 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7287 (mt-10) outliers start: 20 outliers final: 8 residues processed: 134 average time/residue: 0.4956 time to fit residues: 71.3240 Evaluate side-chains 120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 107 optimal weight: 0.0060 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.204432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.161609 restraints weight = 9094.332| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.80 r_work: 0.3568 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9126 Z= 0.122 Angle : 0.511 11.056 12391 Z= 0.270 Chirality : 0.041 0.166 1387 Planarity : 0.004 0.053 1575 Dihedral : 4.163 25.605 1244 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.07 % Allowed : 13.83 % Favored : 84.10 % 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: 1.70 (0.26), residues: 1125 helix: 2.80 (0.24), residues: 443 sheet: -0.28 (0.31), residues: 231 loop : 0.29 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 197 TYR 0.024 0.001 TYR R 191 PHE 0.031 0.001 PHE R 335 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9120) covalent geometry : angle 0.51014 (12379) SS BOND : bond 0.00137 ( 6) SS BOND : angle 1.12792 ( 12) hydrogen bonds : bond 0.03841 ( 499) hydrogen bonds : angle 4.41328 ( 1440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7387 (p0) cc_final: 0.6918 (p0) REVERT: B 134 ARG cc_start: 0.6810 (ptm160) cc_final: 0.6232 (ptm160) REVERT: B 155 ASN cc_start: 0.7763 (t0) cc_final: 0.7513 (m-40) REVERT: B 220 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: N 29 PHE cc_start: 0.7351 (t80) cc_final: 0.7097 (t80) REVERT: R 214 ARG cc_start: 0.7400 (ptm160) cc_final: 0.6972 (pmm150) REVERT: R 390 ARG cc_start: 0.7998 (ttp-110) cc_final: 0.7507 (ttm170) REVERT: R 391 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7309 (mt-10) outliers start: 19 outliers final: 11 residues processed: 128 average time/residue: 0.5123 time to fit residues: 70.4338 Evaluate side-chains 125 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.200466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.156736 restraints weight = 9097.780| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.98 r_work: 0.3501 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9126 Z= 0.189 Angle : 0.585 14.669 12391 Z= 0.305 Chirality : 0.043 0.177 1387 Planarity : 0.004 0.054 1575 Dihedral : 4.458 25.243 1244 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.18 % Allowed : 13.73 % Favored : 84.10 % 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: 1.51 (0.26), residues: 1125 helix: 2.56 (0.24), residues: 443 sheet: -0.29 (0.31), residues: 229 loop : 0.21 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 197 TYR 0.028 0.002 TYR N 60 PHE 0.013 0.002 PHE A 345 TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 9120) covalent geometry : angle 0.58253 (12379) SS BOND : bond 0.00155 ( 6) SS BOND : angle 1.70998 ( 12) hydrogen bonds : bond 0.04335 ( 499) hydrogen bonds : angle 4.64841 ( 1440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7430 (p0) cc_final: 0.7005 (p0) REVERT: B 134 ARG cc_start: 0.6845 (ptm160) cc_final: 0.6223 (ptm160) REVERT: B 155 ASN cc_start: 0.7972 (t0) cc_final: 0.7694 (m-40) REVERT: B 220 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: N 29 PHE cc_start: 0.7449 (t80) cc_final: 0.7248 (t80) REVERT: R 214 ARG cc_start: 0.7386 (ptm160) cc_final: 0.6870 (pmm150) REVERT: R 390 ARG cc_start: 0.8020 (ttp-110) cc_final: 0.7513 (ttm170) REVERT: R 391 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7331 (mt-10) REVERT: R 404 ARG cc_start: 0.6672 (mpt-90) cc_final: 0.5731 (ptm160) outliers start: 20 outliers final: 14 residues processed: 124 average time/residue: 0.5333 time to fit residues: 71.0167 Evaluate side-chains 123 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 101 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.204043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.161293 restraints weight = 9045.154| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.88 r_work: 0.3573 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9126 Z= 0.118 Angle : 0.519 11.763 12391 Z= 0.274 Chirality : 0.040 0.166 1387 Planarity : 0.004 0.057 1575 Dihedral : 4.197 25.343 1244 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.85 % Allowed : 14.60 % Favored : 83.55 % 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: 1.65 (0.26), residues: 1125 helix: 2.75 (0.24), residues: 443 sheet: -0.18 (0.32), residues: 216 loop : 0.17 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 197 TYR 0.025 0.001 TYR N 60 PHE 0.012 0.001 PHE A 212 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9120) covalent geometry : angle 0.51820 (12379) SS BOND : bond 0.00213 ( 6) SS BOND : angle 1.15003 ( 12) hydrogen bonds : bond 0.03812 ( 499) hydrogen bonds : angle 4.43657 ( 1440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7354 (p0) cc_final: 0.6898 (p0) REVERT: B 134 ARG cc_start: 0.6785 (ptm160) cc_final: 0.6195 (ptm160) REVERT: B 155 ASN cc_start: 0.7913 (t0) cc_final: 0.7634 (m-40) REVERT: N 29 PHE cc_start: 0.7352 (t80) cc_final: 0.7069 (t80) REVERT: R 214 ARG cc_start: 0.7365 (ptm160) cc_final: 0.6899 (pmm150) REVERT: R 390 ARG cc_start: 0.8015 (ttp-110) cc_final: 0.7531 (ttm170) outliers start: 17 outliers final: 12 residues processed: 126 average time/residue: 0.5073 time to fit residues: 68.7313 Evaluate side-chains 123 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.203292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.160084 restraints weight = 9069.635| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.98 r_work: 0.3555 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9126 Z= 0.134 Angle : 0.534 12.165 12391 Z= 0.280 Chirality : 0.041 0.188 1387 Planarity : 0.004 0.061 1575 Dihedral : 4.228 24.507 1244 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.96 % Allowed : 14.49 % Favored : 83.55 % 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: 1.63 (0.26), residues: 1125 helix: 2.72 (0.24), residues: 443 sheet: -0.17 (0.32), residues: 216 loop : 0.17 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 197 TYR 0.026 0.001 TYR R 191 PHE 0.012 0.001 PHE A 212 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9120) covalent geometry : angle 0.53230 (12379) SS BOND : bond 0.00131 ( 6) SS BOND : angle 1.33256 ( 12) hydrogen bonds : bond 0.03894 ( 499) hydrogen bonds : angle 4.43969 ( 1440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7383 (p0) cc_final: 0.6940 (p0) REVERT: A 370 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: B 59 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: B 134 ARG cc_start: 0.6775 (ptm160) cc_final: 0.6158 (ptm160) REVERT: B 155 ASN cc_start: 0.7913 (t0) cc_final: 0.7626 (m-40) REVERT: N 29 PHE cc_start: 0.7372 (t80) cc_final: 0.7096 (t80) REVERT: R 214 ARG cc_start: 0.7380 (ptm160) cc_final: 0.6891 (pmm150) REVERT: R 390 ARG cc_start: 0.8007 (ttp-110) cc_final: 0.7515 (ttm170) outliers start: 18 outliers final: 12 residues processed: 121 average time/residue: 0.5342 time to fit residues: 69.3811 Evaluate side-chains 124 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 0.0000 chunk 95 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.205173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.162817 restraints weight = 8971.530| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.76 r_work: 0.3582 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9126 Z= 0.114 Angle : 0.512 10.724 12391 Z= 0.271 Chirality : 0.040 0.165 1387 Planarity : 0.004 0.060 1575 Dihedral : 4.108 24.073 1244 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.63 % Allowed : 14.92 % Favored : 83.44 % 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: 1.69 (0.26), residues: 1125 helix: 2.80 (0.25), residues: 442 sheet: -0.19 (0.32), residues: 218 loop : 0.20 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 197 TYR 0.025 0.001 TYR R 191 PHE 0.013 0.001 PHE R 335 TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9120) covalent geometry : angle 0.51151 (12379) SS BOND : bond 0.00151 ( 6) SS BOND : angle 1.12308 ( 12) hydrogen bonds : bond 0.03729 ( 499) hydrogen bonds : angle 4.34173 ( 1440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3244.17 seconds wall clock time: 56 minutes 1.22 seconds (3361.22 seconds total)