Starting phenix.real_space_refine on Wed Sep 17 08:04:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgg_44512/09_2025/9bgg_44512.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgg_44512/09_2025/9bgg_44512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bgg_44512/09_2025/9bgg_44512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgg_44512/09_2025/9bgg_44512.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bgg_44512/09_2025/9bgg_44512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgg_44512/09_2025/9bgg_44512.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 34 5.16 5 C 4415 2.51 5 N 1186 2.21 5 O 1290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6925 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3417 Classifications: {'peptide': 416} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 2 Chain: "B" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3452 Classifications: {'peptide': 419} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 394} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.81, per 1000 atoms: 0.26 Number of scatterers: 6925 At special positions: 0 Unit cell: (72.864, 101.016, 112.608, 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 34 16.00 O 1290 8.00 N 1186 7.00 C 4415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS B 27 " 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 286 " " NAG A 502 " - " ASN A 406 " " NAG B 501 " - " ASN B 286 " " NAG B 502 " - " ASN B 406 " Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 304.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1610 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 51.7% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 removed outlier: 3.731A pdb=" N TYR A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 90 through 103 removed outlier: 4.220A pdb=" N TYR A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.691A pdb=" N HIS A 142 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.696A pdb=" N ILE A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N HIS A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'A' and resid 240 through 250 Processing helix chain 'A' and resid 250 through 260 removed outlier: 3.667A pdb=" N PHE A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 removed outlier: 3.765A pdb=" N SER A 273 " --> pdb=" O GLN A 269 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.511A pdb=" N VAL A 290 " --> pdb=" O ASN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 315 removed outlier: 3.949A pdb=" N ARG A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 338 removed outlier: 3.777A pdb=" N LEU A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 371 through 382 Processing helix chain 'A' and resid 406 through 420 removed outlier: 3.593A pdb=" N GLY A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 Processing helix chain 'B' and resid 7 through 15 removed outlier: 4.485A pdb=" N TYR B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG B 14 " --> pdb=" O PHE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 42 through 56 Processing helix chain 'B' and resid 90 through 103 removed outlier: 4.034A pdb=" N TYR B 94 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.992A pdb=" N HIS B 142 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 143 " --> pdb=" O LEU B 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 139 through 143' Processing helix chain 'B' and resid 147 through 153 removed outlier: 3.759A pdb=" N ILE B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.996A pdb=" N ILE B 158 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 208 through 224 Processing helix chain 'B' and resid 240 through 250 Processing helix chain 'B' and resid 250 through 260 Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.604A pdb=" N SER B 273 " --> pdb=" O GLN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.839A pdb=" N VAL B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 315 Processing helix chain 'B' and resid 320 through 337 removed outlier: 3.689A pdb=" N LEU B 324 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.561A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 382 Processing helix chain 'B' and resid 406 through 420 Processing helix chain 'B' and resid 437 through 453 Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 132 removed outlier: 6.272A pdb=" N ILE A 109 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 131 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE A 111 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 112 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 33 " --> pdb=" O LYS A 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.376A pdb=" N ALA A 399 " --> pdb=" O CYS A 426 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 185 removed outlier: 4.604A pdb=" N TRP A 196 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 185 removed outlier: 3.606A pdb=" N MET A 393 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 282 through 283 removed outlier: 4.652A pdb=" N LYS A 385 " --> pdb=" O GLN A 283 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 131 removed outlier: 6.661A pdb=" N ILE B 109 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL B 131 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 111 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 34 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL B 112 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR B 36 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP B 33 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU B 168 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL B 35 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 172 through 174 Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 185 removed outlier: 6.954A pdb=" N VAL B 230 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 184 through 185 287 hydrogen bonds defined for protein. 822 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: 0.96 Time building geometry restraints manager: 0.77 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: 2236 1.34 - 1.46: 1243 1.46 - 1.58: 3563 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 7102 Sorted by residual: bond pdb=" C LEU A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.21e+00 bond pdb=" CB ASP A 170 " pdb=" CG ASP A 170 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.89e-01 bond pdb=" CG GLU A 90 " pdb=" CD GLU A 90 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.61e-01 bond pdb=" N ARG A 107 " pdb=" CA ARG A 107 " ideal model delta sigma weight residual 1.460 1.470 -0.010 1.22e-02 6.72e+03 6.57e-01 bond pdb=" C LEU B 143 " pdb=" N PRO B 144 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 6.20e-01 ... (remaining 7097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 9479 1.73 - 3.45: 118 3.45 - 5.18: 16 5.18 - 6.90: 4 6.90 - 8.63: 2 Bond angle restraints: 9619 Sorted by residual: angle pdb=" N GLY A 394 " pdb=" CA GLY A 394 " pdb=" C GLY A 394 " ideal model delta sigma weight residual 110.77 115.68 -4.91 1.59e+00 3.96e-01 9.54e+00 angle pdb=" C PHE B 254 " pdb=" N ASP B 255 " pdb=" CA ASP B 255 " ideal model delta sigma weight residual 120.72 116.22 4.50 1.67e+00 3.59e-01 7.26e+00 angle pdb=" CA LEU B 143 " pdb=" CB LEU B 143 " pdb=" CG LEU B 143 " ideal model delta sigma weight residual 116.30 124.93 -8.63 3.50e+00 8.16e-02 6.08e+00 angle pdb=" CA LEU A 143 " pdb=" CB LEU A 143 " pdb=" CG LEU A 143 " ideal model delta sigma weight residual 116.30 124.88 -8.58 3.50e+00 8.16e-02 6.01e+00 angle pdb=" C PHE B 275 " pdb=" N TYR B 276 " pdb=" CA TYR B 276 " ideal model delta sigma weight residual 121.14 117.31 3.83 1.75e+00 3.27e-01 4.78e+00 ... (remaining 9614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4007 17.87 - 35.73: 271 35.73 - 53.60: 44 53.60 - 71.46: 11 71.46 - 89.33: 8 Dihedral angle restraints: 4341 sinusoidal: 1869 harmonic: 2472 Sorted by residual: dihedral pdb=" CA ASN B 406 " pdb=" C ASN B 406 " pdb=" N VAL B 407 " pdb=" CA VAL B 407 " ideal model delta harmonic sigma weight residual -180.00 -163.00 -17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB GLU A 266 " pdb=" CG GLU A 266 " pdb=" CD GLU A 266 " pdb=" OE1 GLU A 266 " ideal model delta sinusoidal sigma weight residual 0.00 89.33 -89.33 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 100 " pdb=" CG GLU A 100 " pdb=" CD GLU A 100 " pdb=" OE1 GLU A 100 " ideal model delta sinusoidal sigma weight residual 0.00 88.97 -88.97 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 4338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 672 0.032 - 0.065: 249 0.065 - 0.097: 82 0.097 - 0.130: 47 0.130 - 0.162: 1 Chirality restraints: 1051 Sorted by residual: chirality pdb=" C2 NAG B 502 " pdb=" C1 NAG B 502 " pdb=" C3 NAG B 502 " pdb=" N2 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA ILE A 431 " pdb=" N ILE A 431 " pdb=" C ILE A 431 " pdb=" CB ILE A 431 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA VAL A 230 " pdb=" N VAL A 230 " pdb=" C VAL A 230 " pdb=" CB VAL A 230 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 1048 not shown) Planarity restraints: 1244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 408 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.51e+00 pdb=" C SER B 408 " -0.027 2.00e-02 2.50e+03 pdb=" O SER B 408 " 0.010 2.00e-02 2.50e+03 pdb=" N HIS B 409 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 234 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 235 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 234 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO B 235 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 235 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 235 " -0.018 5.00e-02 4.00e+02 ... (remaining 1241 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 528 2.74 - 3.28: 7085 3.28 - 3.82: 11185 3.82 - 4.36: 12963 4.36 - 4.90: 22665 Nonbonded interactions: 54426 Sorted by model distance: nonbonded pdb=" O LEU B 302 " pdb=" OH TYR B 355 " model vdw 2.200 3.040 nonbonded pdb=" NE1 TRP A 105 " pdb=" O VAL A 178 " model vdw 2.212 3.120 nonbonded pdb=" ND2 ASN A 169 " pdb=" OD1 ASP A 171 " model vdw 2.226 3.120 nonbonded pdb=" O PRO A 104 " pdb=" ND2 ASN B 16 " model vdw 2.231 3.120 nonbonded pdb=" NE2 GLN B 190 " pdb=" OD1 ASP B 239 " model vdw 2.242 3.120 ... (remaining 54421 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 6 through 339 or resid 351 through 502)) selection = (chain 'B' and (resid 6 through 56 or resid 89 through 463 or resid 501 through \ 502)) } 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.450 Find NCS groups from input model: 0.130 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 0.026 7107 Z= 0.117 Angle : 0.541 8.627 9633 Z= 0.274 Chirality : 0.042 0.162 1051 Planarity : 0.004 0.038 1240 Dihedral : 12.808 89.327 2728 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.43 (0.30), residues: 823 helix: 1.11 (0.28), residues: 344 sheet: 0.55 (0.58), residues: 97 loop : -0.50 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 93 TYR 0.013 0.001 TYR B 276 PHE 0.010 0.001 PHE B 272 TRP 0.008 0.001 TRP B 196 HIS 0.002 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7102) covalent geometry : angle 0.53335 ( 9619) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.28745 ( 2) hydrogen bonds : bond 0.16513 ( 283) hydrogen bonds : angle 6.36731 ( 822) link_NAG-ASN : bond 0.00487 ( 4) link_NAG-ASN : angle 2.60275 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.281 Fit side-chains REVERT: A 122 ASN cc_start: 0.7890 (t0) cc_final: 0.7685 (t0) REVERT: A 292 ASP cc_start: 0.7905 (m-30) cc_final: 0.7188 (m-30) REVERT: A 330 MET cc_start: 0.7010 (ptp) cc_final: 0.6779 (ptp) REVERT: A 413 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7658 (mm110) REVERT: A 452 MET cc_start: 0.7334 (mmm) cc_final: 0.6946 (mmm) REVERT: B 30 MET cc_start: 0.7611 (mmm) cc_final: 0.7060 (mmp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0916 time to fit residues: 16.8805 Evaluate side-chains 108 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.0470 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 409 HIS A 428 ASN B 16 ASN B 89 ASN B 139 ASN B 190 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.194612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.160676 restraints weight = 9999.244| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.83 r_work: 0.3877 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7107 Z= 0.122 Angle : 0.569 8.085 9633 Z= 0.286 Chirality : 0.044 0.150 1051 Planarity : 0.004 0.039 1240 Dihedral : 4.961 59.923 993 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.28 % Allowed : 10.26 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.52 (0.30), residues: 823 helix: 1.13 (0.28), residues: 354 sheet: 0.61 (0.57), residues: 97 loop : -0.42 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 389 TYR 0.022 0.001 TYR B 276 PHE 0.015 0.001 PHE A 270 TRP 0.013 0.001 TRP A 179 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7102) covalent geometry : angle 0.56679 ( 9619) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.89616 ( 2) hydrogen bonds : bond 0.03738 ( 283) hydrogen bonds : angle 4.76513 ( 822) link_NAG-ASN : bond 0.00513 ( 4) link_NAG-ASN : angle 1.50595 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.263 Fit side-chains REVERT: A 13 TYR cc_start: 0.7382 (m-80) cc_final: 0.7169 (m-10) REVERT: A 249 MET cc_start: 0.7998 (ttt) cc_final: 0.7449 (mtp) REVERT: A 292 ASP cc_start: 0.8010 (m-30) cc_final: 0.7316 (m-30) REVERT: A 429 ASP cc_start: 0.7929 (t0) cc_final: 0.7673 (t70) REVERT: A 452 MET cc_start: 0.7276 (mmm) cc_final: 0.6999 (mmm) REVERT: B 30 MET cc_start: 0.7566 (mmm) cc_final: 0.7048 (mmp) outliers start: 10 outliers final: 4 residues processed: 132 average time/residue: 0.0886 time to fit residues: 15.6234 Evaluate side-chains 114 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 71 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN B 89 ASN B 139 ASN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.190628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.156552 restraints weight = 9963.198| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.80 r_work: 0.3819 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7107 Z= 0.144 Angle : 0.568 8.911 9633 Z= 0.287 Chirality : 0.045 0.167 1051 Planarity : 0.004 0.043 1240 Dihedral : 4.880 55.796 993 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.28 % Allowed : 13.59 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.39 (0.30), residues: 823 helix: 1.11 (0.28), residues: 355 sheet: 0.35 (0.55), residues: 94 loop : -0.54 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.025 0.001 TYR B 276 PHE 0.011 0.001 PHE A 254 TRP 0.011 0.001 TRP A 179 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7102) covalent geometry : angle 0.56607 ( 9619) SS BOND : bond 0.00245 ( 1) SS BOND : angle 0.69607 ( 2) hydrogen bonds : bond 0.03496 ( 283) hydrogen bonds : angle 4.58351 ( 822) link_NAG-ASN : bond 0.00409 ( 4) link_NAG-ASN : angle 1.27758 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.273 Fit side-chains REVERT: A 212 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7013 (tp) REVERT: A 429 ASP cc_start: 0.8118 (t0) cc_final: 0.7888 (t70) REVERT: A 452 MET cc_start: 0.7401 (mmm) cc_final: 0.7119 (mmm) REVERT: B 30 MET cc_start: 0.7653 (mmm) cc_final: 0.7085 (mmp) REVERT: B 393 MET cc_start: 0.7383 (pmm) cc_final: 0.6770 (ptp) REVERT: B 452 MET cc_start: 0.7328 (ttp) cc_final: 0.6928 (ttp) outliers start: 10 outliers final: 7 residues processed: 126 average time/residue: 0.0792 time to fit residues: 13.4973 Evaluate side-chains 116 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 371 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.0020 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 186 HIS ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN A 386 ASN B 190 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 HIS B 435 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.192690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.158757 restraints weight = 10054.458| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.82 r_work: 0.3845 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7107 Z= 0.108 Angle : 0.545 9.095 9633 Z= 0.274 Chirality : 0.043 0.157 1051 Planarity : 0.004 0.042 1240 Dihedral : 4.640 53.976 993 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.28 % Allowed : 14.87 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.45 (0.30), residues: 823 helix: 1.24 (0.28), residues: 356 sheet: 0.18 (0.54), residues: 97 loop : -0.55 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 446 TYR 0.025 0.001 TYR B 276 PHE 0.010 0.001 PHE A 254 TRP 0.010 0.001 TRP A 179 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7102) covalent geometry : angle 0.54316 ( 9619) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.49806 ( 2) hydrogen bonds : bond 0.03031 ( 283) hydrogen bonds : angle 4.42386 ( 822) link_NAG-ASN : bond 0.00354 ( 4) link_NAG-ASN : angle 1.31712 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.275 Fit side-chains REVERT: A 212 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6898 (tp) REVERT: A 398 ILE cc_start: 0.8655 (mp) cc_final: 0.8425 (mp) REVERT: A 452 MET cc_start: 0.7329 (mmm) cc_final: 0.7082 (mmm) REVERT: B 30 MET cc_start: 0.7661 (mmm) cc_final: 0.7132 (mmt) REVERT: B 393 MET cc_start: 0.7296 (pmm) cc_final: 0.7081 (ptp) REVERT: B 452 MET cc_start: 0.7185 (ttp) cc_final: 0.6944 (ttp) outliers start: 10 outliers final: 5 residues processed: 124 average time/residue: 0.0875 time to fit residues: 14.4097 Evaluate side-chains 114 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 364 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 72 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 186 HIS A 247 GLN ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.190841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.156768 restraints weight = 10049.247| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.82 r_work: 0.3835 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7107 Z= 0.123 Angle : 0.554 9.190 9633 Z= 0.281 Chirality : 0.044 0.156 1051 Planarity : 0.004 0.044 1240 Dihedral : 4.642 53.826 993 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.92 % Allowed : 14.62 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.46 (0.30), residues: 823 helix: 1.31 (0.28), residues: 356 sheet: 0.17 (0.54), residues: 94 loop : -0.60 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.027 0.001 TYR B 276 PHE 0.012 0.001 PHE A 254 TRP 0.010 0.001 TRP A 179 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7102) covalent geometry : angle 0.55299 ( 9619) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.44194 ( 2) hydrogen bonds : bond 0.03050 ( 283) hydrogen bonds : angle 4.34797 ( 822) link_NAG-ASN : bond 0.00302 ( 4) link_NAG-ASN : angle 1.25943 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.286 Fit side-chains REVERT: A 212 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7009 (tp) REVERT: A 279 MET cc_start: 0.8527 (mmm) cc_final: 0.8307 (mmm) REVERT: A 452 MET cc_start: 0.7351 (mmm) cc_final: 0.7121 (mmm) REVERT: B 30 MET cc_start: 0.7751 (mmm) cc_final: 0.7200 (mmt) REVERT: B 452 MET cc_start: 0.7240 (ttp) cc_final: 0.6820 (ttp) outliers start: 15 outliers final: 9 residues processed: 128 average time/residue: 0.0855 time to fit residues: 14.7780 Evaluate side-chains 115 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 364 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 186 HIS ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 GLN B 409 HIS B 435 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.189957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155928 restraints weight = 10114.327| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.83 r_work: 0.3817 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7107 Z= 0.129 Angle : 0.564 9.123 9633 Z= 0.287 Chirality : 0.044 0.184 1051 Planarity : 0.004 0.043 1240 Dihedral : 4.618 53.377 993 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.54 % Allowed : 16.54 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.42 (0.30), residues: 823 helix: 1.30 (0.28), residues: 356 sheet: 0.04 (0.54), residues: 94 loop : -0.61 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 446 TYR 0.025 0.001 TYR B 276 PHE 0.026 0.001 PHE B 453 TRP 0.022 0.001 TRP A 196 HIS 0.005 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7102) covalent geometry : angle 0.56239 ( 9619) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.45975 ( 2) hydrogen bonds : bond 0.03112 ( 283) hydrogen bonds : angle 4.31000 ( 822) link_NAG-ASN : bond 0.00285 ( 4) link_NAG-ASN : angle 1.20986 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.224 Fit side-chains REVERT: A 212 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7065 (tp) REVERT: A 452 MET cc_start: 0.7313 (mmm) cc_final: 0.7088 (mmm) REVERT: B 30 MET cc_start: 0.7873 (mmm) cc_final: 0.7246 (mmt) outliers start: 12 outliers final: 10 residues processed: 115 average time/residue: 0.0823 time to fit residues: 12.9339 Evaluate side-chains 109 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 364 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 0.0050 chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 186 HIS ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN B 190 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.190183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.156067 restraints weight = 10006.081| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.82 r_work: 0.3817 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7107 Z= 0.124 Angle : 0.561 9.138 9633 Z= 0.286 Chirality : 0.044 0.155 1051 Planarity : 0.004 0.043 1240 Dihedral : 4.594 53.070 993 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.44 % Allowed : 16.03 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.49 (0.30), residues: 823 helix: 1.40 (0.28), residues: 355 sheet: 0.05 (0.55), residues: 94 loop : -0.61 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 446 TYR 0.026 0.001 TYR A 274 PHE 0.024 0.001 PHE B 453 TRP 0.023 0.001 TRP A 196 HIS 0.005 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7102) covalent geometry : angle 0.55941 ( 9619) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.31561 ( 2) hydrogen bonds : bond 0.03036 ( 283) hydrogen bonds : angle 4.27936 ( 822) link_NAG-ASN : bond 0.00269 ( 4) link_NAG-ASN : angle 1.18955 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.274 Fit side-chains REVERT: A 212 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7111 (tp) REVERT: A 331 LEU cc_start: 0.5357 (OUTLIER) cc_final: 0.5100 (tt) REVERT: A 452 MET cc_start: 0.7275 (mmm) cc_final: 0.6909 (mmt) REVERT: B 30 MET cc_start: 0.7864 (mmm) cc_final: 0.7235 (mmt) outliers start: 19 outliers final: 10 residues processed: 124 average time/residue: 0.0766 time to fit residues: 12.9679 Evaluate side-chains 115 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 364 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN B 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.189692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.156301 restraints weight = 10039.745| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.71 r_work: 0.3819 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7107 Z= 0.134 Angle : 0.575 9.087 9633 Z= 0.293 Chirality : 0.044 0.157 1051 Planarity : 0.004 0.043 1240 Dihedral : 4.653 52.725 993 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.92 % Allowed : 16.79 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.43 (0.30), residues: 823 helix: 1.38 (0.28), residues: 355 sheet: -0.03 (0.55), residues: 94 loop : -0.67 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 389 TYR 0.025 0.001 TYR B 276 PHE 0.040 0.002 PHE B 453 TRP 0.024 0.001 TRP A 196 HIS 0.005 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7102) covalent geometry : angle 0.57341 ( 9619) SS BOND : bond 0.00190 ( 1) SS BOND : angle 0.36289 ( 2) hydrogen bonds : bond 0.03114 ( 283) hydrogen bonds : angle 4.29121 ( 822) link_NAG-ASN : bond 0.00271 ( 4) link_NAG-ASN : angle 1.21310 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.323 Fit side-chains REVERT: A 212 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7200 (tp) REVERT: A 452 MET cc_start: 0.7228 (mmm) cc_final: 0.6848 (mmt) REVERT: B 337 MET cc_start: 0.7960 (ppp) cc_final: 0.5288 (mtt) outliers start: 15 outliers final: 11 residues processed: 122 average time/residue: 0.0832 time to fit residues: 13.7503 Evaluate side-chains 114 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 364 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 0.0870 chunk 49 optimal weight: 2.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.188118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.156299 restraints weight = 9805.437| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.61 r_work: 0.3809 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7107 Z= 0.150 Angle : 0.603 9.246 9633 Z= 0.308 Chirality : 0.045 0.172 1051 Planarity : 0.004 0.043 1240 Dihedral : 4.709 52.460 993 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.67 % Allowed : 17.31 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.32 (0.30), residues: 823 helix: 1.25 (0.28), residues: 357 sheet: -0.10 (0.55), residues: 94 loop : -0.69 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 389 TYR 0.030 0.001 TYR B 276 PHE 0.035 0.002 PHE B 453 TRP 0.023 0.002 TRP A 196 HIS 0.004 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7102) covalent geometry : angle 0.60145 ( 9619) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.69910 ( 2) hydrogen bonds : bond 0.03289 ( 283) hydrogen bonds : angle 4.35129 ( 822) link_NAG-ASN : bond 0.00269 ( 4) link_NAG-ASN : angle 1.21374 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.274 Fit side-chains REVERT: A 212 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7052 (tp) REVERT: A 452 MET cc_start: 0.7258 (mmm) cc_final: 0.7042 (mmm) REVERT: B 327 LEU cc_start: 0.7663 (mt) cc_final: 0.7406 (tt) REVERT: B 337 MET cc_start: 0.7962 (ppp) cc_final: 0.5326 (mtt) outliers start: 13 outliers final: 10 residues processed: 111 average time/residue: 0.0826 time to fit residues: 12.5007 Evaluate side-chains 114 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 364 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 61 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 79 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.189484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.155606 restraints weight = 9995.572| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.81 r_work: 0.3811 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7107 Z= 0.130 Angle : 0.586 9.289 9633 Z= 0.299 Chirality : 0.045 0.167 1051 Planarity : 0.004 0.042 1240 Dihedral : 4.657 52.333 993 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.41 % Allowed : 17.95 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.35 (0.30), residues: 823 helix: 1.26 (0.28), residues: 357 sheet: -0.08 (0.55), residues: 94 loop : -0.66 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 389 TYR 0.029 0.001 TYR B 276 PHE 0.033 0.002 PHE B 453 TRP 0.023 0.001 TRP A 196 HIS 0.008 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7102) covalent geometry : angle 0.58456 ( 9619) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.67780 ( 2) hydrogen bonds : bond 0.03189 ( 283) hydrogen bonds : angle 4.32066 ( 822) link_NAG-ASN : bond 0.00262 ( 4) link_NAG-ASN : angle 1.24053 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.308 Fit side-chains REVERT: A 145 THR cc_start: 0.7933 (p) cc_final: 0.7630 (m) REVERT: A 212 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7199 (tp) REVERT: A 452 MET cc_start: 0.7334 (mmm) cc_final: 0.7120 (mmm) REVERT: B 30 MET cc_start: 0.8065 (mmt) cc_final: 0.7609 (mmt) REVERT: B 337 MET cc_start: 0.7949 (ppp) cc_final: 0.5339 (mtt) REVERT: B 393 MET cc_start: 0.7158 (pmm) cc_final: 0.6835 (ptp) outliers start: 11 outliers final: 10 residues processed: 116 average time/residue: 0.0878 time to fit residues: 13.6937 Evaluate side-chains 114 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 364 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 72 optimal weight: 0.0050 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.190879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.157930 restraints weight = 9958.427| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.70 r_work: 0.3843 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7107 Z= 0.117 Angle : 0.589 9.297 9633 Z= 0.300 Chirality : 0.044 0.164 1051 Planarity : 0.004 0.042 1240 Dihedral : 4.585 52.324 993 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.28 % Allowed : 18.33 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.40 (0.30), residues: 823 helix: 1.32 (0.28), residues: 357 sheet: -0.19 (0.54), residues: 97 loop : -0.60 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 389 TYR 0.028 0.001 TYR B 276 PHE 0.031 0.001 PHE B 453 TRP 0.027 0.001 TRP A 196 HIS 0.006 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7102) covalent geometry : angle 0.58726 ( 9619) SS BOND : bond 0.00050 ( 1) SS BOND : angle 0.58744 ( 2) hydrogen bonds : bond 0.03045 ( 283) hydrogen bonds : angle 4.29186 ( 822) link_NAG-ASN : bond 0.00267 ( 4) link_NAG-ASN : angle 1.26454 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1624.77 seconds wall clock time: 28 minutes 41.71 seconds (1721.71 seconds total)