Starting phenix.real_space_refine on Thu Jul 2 04:17:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g3f_50997/07_2026/9g3f_50997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g3f_50997/07_2026/9g3f_50997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g3f_50997/07_2026/9g3f_50997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g3f_50997/07_2026/9g3f_50997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g3f_50997/07_2026/9g3f_50997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g3f_50997/07_2026/9g3f_50997.map" } resolution = 3.36 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= 0.007 sd= 0.107 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 20 5.16 5 C 4317 2.51 5 N 1015 2.21 5 O 1065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6419 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3200 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 14, 'TRANS': 378} Chain: "B" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3128 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 14, 'TRANS': 370} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 1.00, per 1000 atoms: 0.16 Number of scatterers: 6419 At special positions: 0 Unit cell: (62.342, 105.266, 99.134, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 2 15.00 O 1065 8.00 N 1015 7.00 C 4317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 245.5 milliseconds 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1456 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 2 sheets defined 85.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 11 through 29 removed outlier: 4.680A pdb=" N PHE A 17 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.620A pdb=" N PHE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 78 removed outlier: 3.815A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 88 through 125 removed outlier: 3.507A pdb=" N VAL A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.804A pdb=" N SER A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 175 removed outlier: 3.517A pdb=" N PHE A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 193 through 227 removed outlier: 3.878A pdb=" N ALA A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 263 through 289 removed outlier: 4.378A pdb=" N GLY A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 337 removed outlier: 4.381A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLU A 300 " --> pdb=" O PRO A 296 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 319 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.544A pdb=" N ALA A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 390 removed outlier: 4.412A pdb=" N ARG A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 29 Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.557A pdb=" N ARG B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE B 52 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP B 53 " --> pdb=" O ALA B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 53' Processing helix chain 'B' and resid 54 through 76 removed outlier: 3.833A pdb=" N PHE B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 88 through 125 removed outlier: 3.608A pdb=" N VAL B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix removed outlier: 3.712A pdb=" N SER B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 177 removed outlier: 3.733A pdb=" N PHE B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 193 through 227 removed outlier: 3.528A pdb=" N ARG B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 241 through 254 removed outlier: 3.687A pdb=" N GLY B 254 " --> pdb=" O TRP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 262 removed outlier: 3.608A pdb=" N GLY B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 289 removed outlier: 4.480A pdb=" N GLY B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 289 " --> pdb=" O TYR B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 337 removed outlier: 3.761A pdb=" N GLU B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.621A pdb=" N ALA B 344 " --> pdb=" O PRO B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 371 removed outlier: 3.534A pdb=" N GLY B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR B 368 " --> pdb=" O GLY B 364 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B 370 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 384 removed outlier: 4.038A pdb=" N MET B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 233 removed outlier: 3.533A pdb=" N GLY A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 233 462 hydrogen bonds defined for protein. 1380 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: 0.66 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 991 1.32 - 1.44: 2016 1.44 - 1.56: 3572 1.56 - 1.68: 4 1.68 - 1.80: 38 Bond restraints: 6621 Sorted by residual: bond pdb=" C VAL B 191 " pdb=" O VAL B 191 " ideal model delta sigma weight residual 1.242 1.226 0.016 1.23e-02 6.61e+03 1.73e+00 bond pdb=" C PRO A 295 " pdb=" N PRO A 296 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.14e+00 bond pdb=" N ILE A 45 " pdb=" CA ILE A 45 " ideal model delta sigma weight residual 1.454 1.462 -0.007 7.70e-03 1.69e+04 9.15e-01 bond pdb=" CA HIS B 81 " pdb=" C HIS B 81 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.37e-02 5.33e+03 6.37e-01 bond pdb=" CA VAL B 191 " pdb=" C VAL B 191 " ideal model delta sigma weight residual 1.520 1.531 -0.012 1.47e-02 4.63e+03 6.32e-01 ... (remaining 6616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 8807 1.51 - 3.01: 167 3.01 - 4.52: 30 4.52 - 6.03: 11 6.03 - 7.54: 1 Bond angle restraints: 9016 Sorted by residual: angle pdb=" CA ARG B 82 " pdb=" CB ARG B 82 " pdb=" CG ARG B 82 " ideal model delta sigma weight residual 114.10 119.33 -5.23 2.00e+00 2.50e-01 6.84e+00 angle pdb=" N ALA A 29 " pdb=" CA ALA A 29 " pdb=" C ALA A 29 " ideal model delta sigma weight residual 110.44 107.41 3.03 1.20e+00 6.94e-01 6.36e+00 angle pdb=" N LEU B 369 " pdb=" CA LEU B 369 " pdb=" C LEU B 369 " ideal model delta sigma weight residual 112.93 109.72 3.21 1.33e+00 5.65e-01 5.82e+00 angle pdb=" N GLN B 189 " pdb=" CA GLN B 189 " pdb=" C GLN B 189 " ideal model delta sigma weight residual 114.75 111.72 3.03 1.26e+00 6.30e-01 5.77e+00 angle pdb=" N VAL B 191 " pdb=" CA VAL B 191 " pdb=" C VAL B 191 " ideal model delta sigma weight residual 113.43 110.92 2.51 1.09e+00 8.42e-01 5.28e+00 ... (remaining 9011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 3419 17.83 - 35.66: 252 35.66 - 53.49: 49 53.49 - 71.32: 8 71.32 - 89.15: 3 Dihedral angle restraints: 3731 sinusoidal: 1457 harmonic: 2274 Sorted by residual: dihedral pdb=" CA ALA B 188 " pdb=" C ALA B 188 " pdb=" N GLN B 189 " pdb=" CA GLN B 189 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB GLU B 282 " pdb=" CG GLU B 282 " pdb=" CD GLU B 282 " pdb=" OE1 GLU B 282 " ideal model delta sinusoidal sigma weight residual 0.00 89.15 -89.15 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ALA A 176 " pdb=" C ALA A 176 " pdb=" N ASN A 177 " pdb=" CA ASN A 177 " ideal model delta harmonic sigma weight residual 180.00 164.39 15.61 0 5.00e+00 4.00e-02 9.75e+00 ... (remaining 3728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 575 0.027 - 0.054: 281 0.054 - 0.081: 99 0.081 - 0.109: 33 0.109 - 0.136: 9 Chirality restraints: 997 Sorted by residual: chirality pdb=" CA VAL A 129 " pdb=" N VAL A 129 " pdb=" C VAL A 129 " pdb=" CB VAL A 129 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA PRO A 234 " pdb=" N PRO A 234 " pdb=" C PRO A 234 " pdb=" CB PRO A 234 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA ILE B 239 " pdb=" N ILE B 239 " pdb=" C ILE B 239 " pdb=" CB ILE B 239 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 994 not shown) Planarity restraints: 1096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 295 " 0.031 5.00e-02 4.00e+02 4.63e-02 3.42e+00 pdb=" N PRO B 296 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 295 " -0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 296 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 82 " -0.008 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C ARG B 82 " 0.026 2.00e-02 2.50e+03 pdb=" O ARG B 82 " -0.010 2.00e-02 2.50e+03 pdb=" N TRP B 83 " -0.009 2.00e-02 2.50e+03 ... (remaining 1093 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1531 2.78 - 3.31: 6372 3.31 - 3.84: 10278 3.84 - 4.37: 12336 4.37 - 4.90: 20993 Nonbonded interactions: 51510 Sorted by model distance: nonbonded pdb=" O4P PGT A 501 " pdb=" O6 PGT A 501 " model vdw 2.249 3.040 nonbonded pdb=" O ILE A 38 " pdb=" OG1 THR A 39 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR A 91 " pdb=" OH TYR A 162 " model vdw 2.355 3.040 nonbonded pdb=" O ARG B 197 " pdb=" OG1 THR B 201 " model vdw 2.357 3.040 nonbonded pdb=" OE1 GLN A 179 " pdb=" NH2 ARG A 182 " model vdw 2.361 3.120 ... (remaining 51505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 386 or (resid 501 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 or n \ ame C44 or name C45 or name C46 or name C5 or name C6 or name O11 or name O1P or \ name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name O5 o \ r name O6 or name P )))) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.250 Find NCS groups from input model: 0.110 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6621 Z= 0.125 Angle : 0.541 7.537 9016 Z= 0.313 Chirality : 0.037 0.136 997 Planarity : 0.004 0.046 1096 Dihedral : 13.306 89.149 2275 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.28), residues: 774 helix: -0.92 (0.19), residues: 626 sheet: None (None), residues: 0 loop : -1.71 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 292 TYR 0.015 0.001 TYR A 78 PHE 0.019 0.001 PHE A 57 TRP 0.009 0.001 TRP A 53 HIS 0.008 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 6621) covalent geometry : angle 0.54105 / 0.31 ( 9016) hydrogen bonds : bond 0.25070 / 16.37 ( 462) hydrogen bonds : angle 8.14182 / 5.86 ( 1380) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.150 Fit side-chains REVERT: A 318 TYR cc_start: 0.7813 (m-10) cc_final: 0.6944 (m-10) REVERT: A 352 MET cc_start: 0.8638 (ttp) cc_final: 0.8310 (ttt) REVERT: B 318 TYR cc_start: 0.7908 (m-10) cc_final: 0.6903 (m-10) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0624 time to fit residues: 6.4511 Evaluate side-chains 68 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 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 = 0.3677 r_free = 0.3677 target = 0.146761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115528 restraints weight = 7726.201| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.84 r_work: 0.3157 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6621 Z= 0.152 Angle : 0.571 8.184 9016 Z= 0.310 Chirality : 0.040 0.128 997 Planarity : 0.004 0.043 1096 Dihedral : 6.104 55.386 910 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.46 % Allowed : 6.40 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.29), residues: 774 helix: 0.26 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.78 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 167 TYR 0.011 0.001 TYR B 162 PHE 0.016 0.002 PHE A 164 TRP 0.013 0.001 TRP A 34 HIS 0.008 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 6621) covalent geometry : angle 0.57080 / 0.31 ( 9016) hydrogen bonds : bond 0.06026 / 3.97 ( 462) hydrogen bonds : angle 4.66302 / 3.40 ( 1380) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.181 Fit side-chains REVERT: A 13 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.6107 (m-80) REVERT: A 330 ASP cc_start: 0.8564 (t0) cc_final: 0.8198 (t0) REVERT: B 330 ASP cc_start: 0.8559 (t0) cc_final: 0.8177 (t0) REVERT: B 346 THR cc_start: 0.8897 (m) cc_final: 0.8659 (p) outliers start: 3 outliers final: 1 residues processed: 72 average time/residue: 0.0602 time to fit residues: 5.8989 Evaluate side-chains 67 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain B residue 257 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 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 = 0.3670 r_free = 0.3670 target = 0.145764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113715 restraints weight = 7767.177| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.93 r_work: 0.3151 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6621 Z= 0.140 Angle : 0.525 7.299 9016 Z= 0.282 Chirality : 0.040 0.129 997 Planarity : 0.004 0.042 1096 Dihedral : 5.989 53.929 910 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.91 % Allowed : 8.23 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.30), residues: 774 helix: 0.66 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.74 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.012 0.001 TYR B 162 PHE 0.015 0.001 PHE A 164 TRP 0.011 0.001 TRP A 34 HIS 0.007 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 6621) covalent geometry : angle 0.52511 / 0.28 ( 9016) hydrogen bonds : bond 0.05081 / 3.35 ( 462) hydrogen bonds : angle 4.21998 / 3.10 ( 1380) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.156 Fit side-chains REVERT: A 13 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.6290 (m-80) REVERT: A 56 ASP cc_start: 0.8802 (t0) cc_final: 0.8181 (t0) REVERT: A 128 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8515 (ttmm) REVERT: A 318 TYR cc_start: 0.7459 (m-10) cc_final: 0.7256 (m-10) REVERT: A 390 GLU cc_start: 0.6737 (tm-30) cc_final: 0.6481 (tm-30) REVERT: B 282 GLU cc_start: 0.7189 (tp30) cc_final: 0.6567 (tp30) REVERT: B 301 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6470 (mt) REVERT: B 330 ASP cc_start: 0.8494 (t0) cc_final: 0.8245 (t0) outliers start: 6 outliers final: 1 residues processed: 70 average time/residue: 0.0561 time to fit residues: 5.4094 Evaluate side-chains 67 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 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 = 0.3668 r_free = 0.3668 target = 0.145663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113459 restraints weight = 7931.388| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.95 r_work: 0.3146 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6621 Z= 0.142 Angle : 0.526 11.223 9016 Z= 0.279 Chirality : 0.039 0.129 997 Planarity : 0.004 0.042 1096 Dihedral : 5.980 58.422 910 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.22 % Allowed : 10.06 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.30), residues: 774 helix: 0.80 (0.20), residues: 637 sheet: None (None), residues: 0 loop : -1.72 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.016 0.001 TYR A 316 PHE 0.015 0.001 PHE A 164 TRP 0.011 0.001 TRP A 34 HIS 0.006 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6621) covalent geometry : angle 0.52647 / 0.28 ( 9016) hydrogen bonds : bond 0.04821 / 3.18 ( 462) hydrogen bonds : angle 4.08891 / 3.01 ( 1380) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.138 Fit side-chains REVERT: A 13 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: A 56 ASP cc_start: 0.8907 (t0) cc_final: 0.8275 (t0) REVERT: A 128 LYS cc_start: 0.8898 (ttpt) cc_final: 0.8570 (ttmm) REVERT: B 282 GLU cc_start: 0.7185 (tp30) cc_final: 0.6627 (tp30) REVERT: B 301 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6502 (mt) REVERT: B 330 ASP cc_start: 0.8346 (t0) cc_final: 0.8124 (t0) outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.0582 time to fit residues: 5.9910 Evaluate side-chains 76 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.147618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116222 restraints weight = 7835.163| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.90 r_work: 0.3195 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6621 Z= 0.118 Angle : 0.492 7.718 9016 Z= 0.261 Chirality : 0.038 0.127 997 Planarity : 0.003 0.043 1096 Dihedral : 5.666 51.694 910 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.68 % Allowed : 9.30 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.30), residues: 774 helix: 1.05 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -1.79 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 167 TYR 0.010 0.001 TYR B 162 PHE 0.013 0.001 PHE A 164 TRP 0.011 0.001 TRP A 34 HIS 0.006 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 6621) covalent geometry : angle 0.49165 / 0.26 ( 9016) hydrogen bonds : bond 0.04322 / 2.86 ( 462) hydrogen bonds : angle 3.89653 / 2.87 ( 1380) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.173 Fit side-chains REVERT: A 13 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: A 56 ASP cc_start: 0.8913 (t0) cc_final: 0.8204 (t0) REVERT: A 78 TYR cc_start: 0.7495 (t80) cc_final: 0.7258 (t80) REVERT: A 252 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6181 (tt) REVERT: A 316 TYR cc_start: 0.7686 (t80) cc_final: 0.7250 (t80) REVERT: B 34 TRP cc_start: 0.7223 (t-100) cc_final: 0.6988 (t-100) REVERT: B 282 GLU cc_start: 0.7284 (tp30) cc_final: 0.6727 (tp30) outliers start: 11 outliers final: 6 residues processed: 82 average time/residue: 0.0536 time to fit residues: 6.4003 Evaluate side-chains 77 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 294 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 62 optimal weight: 0.0270 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 273 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 = 0.3670 r_free = 0.3670 target = 0.145653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113590 restraints weight = 7977.593| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.95 r_work: 0.3158 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6621 Z= 0.137 Angle : 0.517 8.032 9016 Z= 0.274 Chirality : 0.039 0.128 997 Planarity : 0.004 0.053 1096 Dihedral : 5.643 48.302 910 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.83 % Allowed : 9.91 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.30), residues: 774 helix: 1.02 (0.20), residues: 637 sheet: None (None), residues: 0 loop : -1.76 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 167 TYR 0.014 0.001 TYR B 162 PHE 0.015 0.001 PHE A 164 TRP 0.011 0.001 TRP A 34 HIS 0.006 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 6621) covalent geometry : angle 0.51708 / 0.27 ( 9016) hydrogen bonds : bond 0.04574 / 3.02 ( 462) hydrogen bonds : angle 3.97179 / 2.91 ( 1380) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.154 Fit side-chains REVERT: A 13 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: A 56 ASP cc_start: 0.8942 (t0) cc_final: 0.8186 (t0) REVERT: A 78 TYR cc_start: 0.7475 (t80) cc_final: 0.7250 (t80) REVERT: A 252 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6086 (tt) REVERT: A 316 TYR cc_start: 0.7725 (t80) cc_final: 0.7223 (t80) REVERT: B 282 GLU cc_start: 0.7233 (tp30) cc_final: 0.6727 (tp30) outliers start: 12 outliers final: 9 residues processed: 76 average time/residue: 0.0491 time to fit residues: 5.3207 Evaluate side-chains 80 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 294 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 44 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 chunk 43 optimal weight: 0.0980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 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 = 0.3703 r_free = 0.3703 target = 0.148623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116879 restraints weight = 7882.977| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.92 r_work: 0.3201 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6621 Z= 0.114 Angle : 0.487 6.237 9016 Z= 0.260 Chirality : 0.038 0.124 997 Planarity : 0.004 0.048 1096 Dihedral : 5.320 46.195 910 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.37 % Allowed : 10.67 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.30), residues: 774 helix: 1.20 (0.20), residues: 637 sheet: None (None), residues: 0 loop : -1.80 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 167 TYR 0.009 0.001 TYR B 162 PHE 0.014 0.001 PHE A 164 TRP 0.010 0.001 TRP A 53 HIS 0.006 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 6621) covalent geometry : angle 0.48693 / 0.26 ( 9016) hydrogen bonds : bond 0.04164 / 2.76 ( 462) hydrogen bonds : angle 3.81565 / 2.80 ( 1380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.161 Fit side-chains REVERT: A 13 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.6748 (m-80) REVERT: A 56 ASP cc_start: 0.8897 (t0) cc_final: 0.8199 (t0) REVERT: A 78 TYR cc_start: 0.7500 (t80) cc_final: 0.7240 (t80) REVERT: A 252 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.6194 (tt) REVERT: A 316 TYR cc_start: 0.7681 (t80) cc_final: 0.7241 (t80) REVERT: B 282 GLU cc_start: 0.7239 (tp30) cc_final: 0.6787 (tp30) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.0482 time to fit residues: 5.4860 Evaluate side-chains 77 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 294 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 4 optimal weight: 0.0050 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 0.0570 overall best weight: 0.7514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 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 = 0.3672 r_free = 0.3672 target = 0.145867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113758 restraints weight = 7909.871| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.93 r_work: 0.3159 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6621 Z= 0.139 Angle : 0.532 13.067 9016 Z= 0.277 Chirality : 0.039 0.127 997 Planarity : 0.004 0.057 1096 Dihedral : 5.400 45.102 910 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.97 % Favored : 96.90 % Rotamer: Outliers : 2.29 % Allowed : 9.76 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.30), residues: 774 helix: 1.11 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.57 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 167 TYR 0.014 0.001 TYR B 162 PHE 0.014 0.001 PHE A 164 TRP 0.010 0.001 TRP B 34 HIS 0.006 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6621) covalent geometry : angle 0.53205 / 0.28 ( 9016) hydrogen bonds : bond 0.04508 / 2.98 ( 462) hydrogen bonds : angle 3.90956 / 2.87 ( 1380) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.131 Fit side-chains REVERT: A 13 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: A 56 ASP cc_start: 0.8990 (t0) cc_final: 0.8277 (t0) REVERT: A 78 TYR cc_start: 0.7490 (t80) cc_final: 0.7247 (t80) REVERT: A 128 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8497 (ttmm) REVERT: A 131 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6412 (mp) REVERT: A 252 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6153 (tt) REVERT: B 282 GLU cc_start: 0.7233 (tp30) cc_final: 0.6764 (tp30) outliers start: 15 outliers final: 9 residues processed: 79 average time/residue: 0.0527 time to fit residues: 5.9638 Evaluate side-chains 79 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 294 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 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 = 0.3675 r_free = 0.3675 target = 0.146009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113910 restraints weight = 7963.893| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.95 r_work: 0.3140 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6621 Z= 0.137 Angle : 0.525 10.543 9016 Z= 0.276 Chirality : 0.039 0.138 997 Planarity : 0.004 0.052 1096 Dihedral : 5.361 44.167 910 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.84 % Favored : 97.03 % Rotamer: Outliers : 1.83 % Allowed : 10.37 % Favored : 87.80 % 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 are not related in a simple way. whole: 0.95 (0.30), residues: 774 helix: 1.14 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -1.50 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.015 0.001 TYR A 316 PHE 0.013 0.001 PHE A 164 TRP 0.010 0.001 TRP B 34 HIS 0.006 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 6621) covalent geometry : angle 0.52500 / 0.28 ( 9016) hydrogen bonds : bond 0.04499 / 2.98 ( 462) hydrogen bonds : angle 3.90327 / 2.87 ( 1380) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.217 Fit side-chains REVERT: A 13 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: A 56 ASP cc_start: 0.9035 (t0) cc_final: 0.8298 (t0) REVERT: A 78 TYR cc_start: 0.7416 (t80) cc_final: 0.7184 (t80) REVERT: A 131 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6441 (mp) REVERT: A 252 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5973 (tt) REVERT: B 282 GLU cc_start: 0.7125 (tp30) cc_final: 0.6653 (tp30) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.0477 time to fit residues: 5.0453 Evaluate side-chains 77 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 294 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 29 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 0.0770 chunk 37 optimal weight: 5.9990 chunk 26 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 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 = 0.3710 r_free = 0.3710 target = 0.151125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126991 restraints weight = 7704.769| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.29 r_work: 0.3255 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6621 Z= 0.109 Angle : 0.488 9.131 9016 Z= 0.258 Chirality : 0.037 0.121 997 Planarity : 0.004 0.046 1096 Dihedral : 5.002 40.571 910 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.71 % Favored : 97.16 % Rotamer: Outliers : 1.52 % Allowed : 10.82 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.30), residues: 774 helix: 1.34 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -1.48 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 167 TYR 0.008 0.001 TYR A 162 PHE 0.013 0.001 PHE A 164 TRP 0.010 0.001 TRP A 53 HIS 0.006 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 6621) covalent geometry : angle 0.48835 / 0.26 ( 9016) hydrogen bonds : bond 0.03934 / 2.60 ( 462) hydrogen bonds : angle 3.72472 / 2.74 ( 1380) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.215 Fit side-chains REVERT: A 13 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7114 (m-80) REVERT: A 56 ASP cc_start: 0.8949 (t0) cc_final: 0.8304 (t0) REVERT: A 78 TYR cc_start: 0.7801 (t80) cc_final: 0.7569 (t80) REVERT: A 131 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6726 (mp) REVERT: A 316 TYR cc_start: 0.8019 (t80) cc_final: 0.7481 (t80) REVERT: B 282 GLU cc_start: 0.7718 (tp30) cc_final: 0.7414 (tp30) outliers start: 10 outliers final: 7 residues processed: 69 average time/residue: 0.0622 time to fit residues: 6.2354 Evaluate side-chains 69 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 294 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 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 = 0.3674 r_free = 0.3674 target = 0.147849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124255 restraints weight = 7696.719| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.32 r_work: 0.3098 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6621 Z= 0.129 Angle : 0.511 8.647 9016 Z= 0.269 Chirality : 0.039 0.124 997 Planarity : 0.004 0.045 1096 Dihedral : 5.103 40.376 910 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.84 % Favored : 97.03 % Rotamer: Outliers : 1.52 % Allowed : 10.82 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.30), residues: 774 helix: 1.31 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -1.34 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 167 TYR 0.013 0.001 TYR B 162 PHE 0.014 0.001 PHE A 164 TRP 0.009 0.001 TRP A 34 HIS 0.006 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6621) covalent geometry : angle 0.51062 / 0.27 ( 9016) hydrogen bonds : bond 0.04299 / 2.84 ( 462) hydrogen bonds : angle 3.81398 / 2.81 ( 1380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1179.53 seconds wall clock time: 20 minutes 47.78 seconds (1247.78 seconds total)