Starting phenix.real_space_refine on Mon Apr 28 04:11:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgg_44512/04_2025/9bgg_44512.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgg_44512/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bgg_44512/04_2025/9bgg_44512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgg_44512/04_2025/9bgg_44512.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgg_44512/04_2025/9bgg_44512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgg_44512/04_2025/9bgg_44512.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.65, per 1000 atoms: 0.67 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: 1.55 Conformation dependent library (CDL) restraints added in 905.6 milliseconds 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: 0.84 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: 1.91 Time building geometry restraints manager: 1.87 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 463 or resid 501 throug \ h 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: 1.700 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.450 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- 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 : 8.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP B 196 HIS 0.002 0.001 HIS A 435 PHE 0.010 0.001 PHE B 272 TYR 0.013 0.001 TYR B 276 ARG 0.002 0.000 ARG A 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 4) link_NAG-ASN : angle 2.60275 ( 12) hydrogen bonds : bond 0.16513 ( 283) hydrogen bonds : angle 6.36731 ( 822) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.28745 ( 2) covalent geometry : bond 0.00252 ( 7102) covalent geometry : angle 0.53335 ( 9619) *********************** 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 : 0.851 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: 0.7052 (mmp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2175 time to fit residues: 40.0564 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 : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 0.0060 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 428 ASN B 16 ASN B 89 ASN B 190 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.194020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.160879 restraints weight = 9929.736| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.68 r_work: 0.3876 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7107 Z= 0.132 Angle : 0.576 7.910 9633 Z= 0.292 Chirality : 0.044 0.154 1051 Planarity : 0.004 0.038 1240 Dihedral : 4.984 59.853 993 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.30), residues: 823 helix: 1.14 (0.28), residues: 353 sheet: 0.55 (0.56), residues: 97 loop : -0.45 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 179 HIS 0.004 0.001 HIS B 329 PHE 0.019 0.001 PHE A 270 TYR 0.023 0.001 TYR B 276 ARG 0.004 0.000 ARG A 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 4) link_NAG-ASN : angle 1.52241 ( 12) hydrogen bonds : bond 0.03698 ( 283) hydrogen bonds : angle 4.79336 ( 822) SS BOND : bond 0.00186 ( 1) SS BOND : angle 0.95917 ( 2) covalent geometry : bond 0.00288 ( 7102) covalent geometry : angle 0.57410 ( 9619) *********************** 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 133 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.855 Fit side-chains REVERT: A 13 TYR cc_start: 0.7313 (m-80) cc_final: 0.7074 (m-10) REVERT: A 249 MET cc_start: 0.8009 (ttt) cc_final: 0.7462 (mtp) REVERT: A 292 ASP cc_start: 0.8000 (m-30) cc_final: 0.7316 (m-30) REVERT: A 429 ASP cc_start: 0.7892 (t0) cc_final: 0.7646 (t70) REVERT: A 452 MET cc_start: 0.7254 (mmm) cc_final: 0.6980 (mmm) REVERT: B 30 MET cc_start: 0.7551 (mmm) cc_final: 0.7014 (mmp) outliers start: 10 outliers final: 4 residues processed: 129 average time/residue: 0.1991 time to fit residues: 34.2488 Evaluate side-chains 112 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 8 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 71 optimal weight: 0.0670 chunk 61 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 A 386 ASN B 89 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 = 0.4362 r_free = 0.4362 target = 0.193520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.159544 restraints weight = 10018.565| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.82 r_work: 0.3855 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1547 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= 0.115 Angle : 0.537 8.261 9633 Z= 0.271 Chirality : 0.044 0.150 1051 Planarity : 0.004 0.042 1240 Dihedral : 4.699 56.005 993 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.15 % Allowed : 12.95 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.30), residues: 823 helix: 1.22 (0.28), residues: 354 sheet: 0.38 (0.55), residues: 97 loop : -0.45 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 179 HIS 0.003 0.001 HIS A 154 PHE 0.009 0.001 PHE A 254 TYR 0.024 0.001 TYR B 276 ARG 0.004 0.000 ARG A 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 4) link_NAG-ASN : angle 1.28256 ( 12) hydrogen bonds : bond 0.03236 ( 283) hydrogen bonds : angle 4.52414 ( 822) SS BOND : bond 0.00154 ( 1) SS BOND : angle 0.54348 ( 2) covalent geometry : bond 0.00260 ( 7102) covalent geometry : angle 0.53550 ( 9619) *********************** 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 133 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.745 Fit side-chains REVERT: A 212 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6814 (tp) REVERT: A 429 ASP cc_start: 0.8042 (t0) cc_final: 0.7820 (t70) REVERT: A 452 MET cc_start: 0.7378 (mmm) cc_final: 0.7102 (mmm) REVERT: B 30 MET cc_start: 0.7615 (mmm) cc_final: 0.7098 (mmp) REVERT: B 393 MET cc_start: 0.7196 (pmm) cc_final: 0.6514 (ptp) REVERT: B 452 MET cc_start: 0.7290 (ttp) cc_final: 0.6993 (ttp) outliers start: 9 outliers final: 6 residues processed: 129 average time/residue: 0.1930 time to fit residues: 33.1457 Evaluate side-chains 121 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 0.0170 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 A 386 ASN B 190 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 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 = 0.4345 r_free = 0.4345 target = 0.191875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.157646 restraints weight = 10114.342| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.84 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: 0.7504 moved from start: 0.1798 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= 0.124 Angle : 0.553 8.920 9633 Z= 0.279 Chirality : 0.044 0.155 1051 Planarity : 0.004 0.043 1240 Dihedral : 4.655 54.181 993 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.67 % Allowed : 14.23 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.30), residues: 823 helix: 1.26 (0.28), residues: 355 sheet: 0.35 (0.54), residues: 94 loop : -0.57 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 179 HIS 0.003 0.001 HIS B 329 PHE 0.011 0.001 PHE A 254 TYR 0.023 0.001 TYR B 276 ARG 0.003 0.000 ARG B 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 4) link_NAG-ASN : angle 1.27313 ( 12) hydrogen bonds : bond 0.03130 ( 283) hydrogen bonds : angle 4.40726 ( 822) SS BOND : bond 0.00167 ( 1) SS BOND : angle 0.56725 ( 2) covalent geometry : bond 0.00288 ( 7102) covalent geometry : angle 0.55189 ( 9619) *********************** 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 134 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.855 Fit side-chains REVERT: A 212 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6947 (tp) REVERT: A 429 ASP cc_start: 0.8168 (t0) cc_final: 0.7954 (t70) REVERT: A 452 MET cc_start: 0.7383 (mmm) cc_final: 0.7131 (mmm) REVERT: B 30 MET cc_start: 0.7646 (mmm) cc_final: 0.7095 (mmp) REVERT: B 393 MET cc_start: 0.7205 (pmm) cc_final: 0.6972 (ptp) REVERT: B 452 MET cc_start: 0.7241 (ttp) cc_final: 0.6968 (ttp) outliers start: 13 outliers final: 7 residues processed: 129 average time/residue: 0.2475 time to fit residues: 42.9450 Evaluate side-chains 117 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain B residue 158 ILE 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 18 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 409 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 = 0.4344 r_free = 0.4344 target = 0.191681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.158229 restraints weight = 9937.162| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.72 r_work: 0.3844 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2031 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= 0.121 Angle : 0.554 9.132 9633 Z= 0.280 Chirality : 0.044 0.151 1051 Planarity : 0.004 0.042 1240 Dihedral : 4.611 53.884 993 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.54 % Allowed : 14.74 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.30), residues: 823 helix: 1.36 (0.28), residues: 355 sheet: 0.23 (0.54), residues: 94 loop : -0.57 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.004 0.001 HIS B 329 PHE 0.011 0.001 PHE A 254 TYR 0.023 0.001 TYR A 274 ARG 0.002 0.000 ARG B 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 4) link_NAG-ASN : angle 1.27057 ( 12) hydrogen bonds : bond 0.03041 ( 283) hydrogen bonds : angle 4.32465 ( 822) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.43478 ( 2) covalent geometry : bond 0.00279 ( 7102) covalent geometry : angle 0.55218 ( 9619) *********************** 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 130 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.515 Fit side-chains REVERT: A 212 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6975 (tp) REVERT: A 429 ASP cc_start: 0.8232 (t0) cc_final: 0.8022 (t70) REVERT: A 452 MET cc_start: 0.7333 (mmm) cc_final: 0.7099 (mmm) REVERT: B 30 MET cc_start: 0.7690 (mmm) cc_final: 0.7131 (mmt) outliers start: 12 outliers final: 8 residues processed: 124 average time/residue: 0.3081 time to fit residues: 52.5607 Evaluate side-chains 113 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 247 GLN ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 GLN ** B 409 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 = 0.4295 r_free = 0.4295 target = 0.187010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152449 restraints weight = 10057.274| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.84 r_work: 0.3772 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7107 Z= 0.183 Angle : 0.614 9.181 9633 Z= 0.314 Chirality : 0.046 0.186 1051 Planarity : 0.004 0.045 1240 Dihedral : 4.928 53.101 993 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.05 % Allowed : 16.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.30), residues: 823 helix: 1.20 (0.28), residues: 355 sheet: -0.08 (0.53), residues: 94 loop : -0.67 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 196 HIS 0.004 0.001 HIS B 329 PHE 0.024 0.002 PHE A 137 TYR 0.026 0.002 TYR B 276 ARG 0.003 0.000 ARG A 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 4) link_NAG-ASN : angle 1.22335 ( 12) hydrogen bonds : bond 0.03552 ( 283) hydrogen bonds : angle 4.42793 ( 822) SS BOND : bond 0.00198 ( 1) SS BOND : angle 0.39987 ( 2) covalent geometry : bond 0.00437 ( 7102) covalent geometry : angle 0.61250 ( 9619) *********************** 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 126 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.094 Fit side-chains REVERT: A 212 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7161 (tp) REVERT: A 452 MET cc_start: 0.7363 (mmm) cc_final: 0.7132 (mmm) REVERT: B 30 MET cc_start: 0.7853 (mmm) cc_final: 0.7201 (mmp) outliers start: 16 outliers final: 11 residues processed: 118 average time/residue: 0.2289 time to fit residues: 37.7732 Evaluate side-chains 113 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER 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 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 145 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 309 THR 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 2 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** B 190 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN B 409 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.188617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.154946 restraints weight = 9864.901| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.70 r_work: 0.3810 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2530 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= 0.133 Angle : 0.579 9.296 9633 Z= 0.291 Chirality : 0.044 0.170 1051 Planarity : 0.004 0.043 1240 Dihedral : 4.780 52.823 993 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.67 % Allowed : 17.44 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.30), residues: 823 helix: 1.29 (0.28), residues: 355 sheet: -0.22 (0.54), residues: 97 loop : -0.64 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 196 HIS 0.008 0.001 HIS B 329 PHE 0.039 0.002 PHE B 453 TYR 0.029 0.001 TYR B 276 ARG 0.004 0.000 ARG A 446 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 4) link_NAG-ASN : angle 1.26793 ( 12) hydrogen bonds : bond 0.03207 ( 283) hydrogen bonds : angle 4.37449 ( 822) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.65972 ( 2) covalent geometry : bond 0.00309 ( 7102) covalent geometry : angle 0.57782 ( 9619) *********************** 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 127 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.727 Fit side-chains REVERT: A 212 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7187 (tp) REVERT: A 452 MET cc_start: 0.7343 (mmm) cc_final: 0.7116 (mmm) REVERT: B 30 MET cc_start: 0.7801 (mmm) cc_final: 0.7132 (mmt) outliers start: 13 outliers final: 9 residues processed: 122 average time/residue: 0.1936 time to fit residues: 31.9979 Evaluate side-chains 113 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 5 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 53 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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** ** B 260 HIS ** 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 = 0.4319 r_free = 0.4319 target = 0.189261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.155351 restraints weight = 9910.557| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.78 r_work: 0.3801 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2641 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= 0.130 Angle : 0.580 9.248 9633 Z= 0.293 Chirality : 0.045 0.178 1051 Planarity : 0.004 0.043 1240 Dihedral : 4.717 52.675 993 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.18 % Allowed : 17.05 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.30), residues: 823 helix: 1.38 (0.28), residues: 355 sheet: -0.11 (0.55), residues: 94 loop : -0.67 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 196 HIS 0.005 0.001 HIS B 329 PHE 0.032 0.002 PHE B 453 TYR 0.027 0.001 TYR A 274 ARG 0.007 0.000 ARG A 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 4) link_NAG-ASN : angle 1.26204 ( 12) hydrogen bonds : bond 0.03135 ( 283) hydrogen bonds : angle 4.34358 ( 822) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.64899 ( 2) covalent geometry : bond 0.00304 ( 7102) covalent geometry : angle 0.57855 ( 9619) *********************** 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 128 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.790 Fit side-chains REVERT: A 212 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7213 (tp) REVERT: A 452 MET cc_start: 0.7336 (mmm) cc_final: 0.7111 (mmm) REVERT: B 30 MET cc_start: 0.7836 (mmm) cc_final: 0.7176 (mmt) REVERT: B 337 MET cc_start: 0.7954 (ppp) cc_final: 0.5332 (mtt) outliers start: 17 outliers final: 10 residues processed: 123 average time/residue: 0.1847 time to fit residues: 31.1054 Evaluate side-chains 115 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 292 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.0670 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- 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** ** B 260 HIS ** 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 = 0.4291 r_free = 0.4291 target = 0.186585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.152228 restraints weight = 10089.063| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.82 r_work: 0.3760 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7107 Z= 0.173 Angle : 0.626 9.296 9633 Z= 0.319 Chirality : 0.046 0.176 1051 Planarity : 0.004 0.044 1240 Dihedral : 4.857 52.170 993 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.30), residues: 823 helix: 1.28 (0.28), residues: 357 sheet: -0.23 (0.54), residues: 94 loop : -0.72 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 196 HIS 0.005 0.001 HIS B 329 PHE 0.031 0.002 PHE B 453 TYR 0.028 0.001 TYR A 274 ARG 0.006 0.000 ARG A 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 4) link_NAG-ASN : angle 1.31827 ( 12) hydrogen bonds : bond 0.03449 ( 283) hydrogen bonds : angle 4.44027 ( 822) SS BOND : bond 0.00087 ( 1) SS BOND : angle 0.66503 ( 2) covalent geometry : bond 0.00414 ( 7102) covalent geometry : angle 0.62470 ( 9619) *********************** 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 122 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.997 Fit side-chains REVERT: A 212 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7206 (tp) REVERT: A 452 MET cc_start: 0.7340 (mmm) cc_final: 0.7127 (mmm) REVERT: B 30 MET cc_start: 0.7884 (mmm) cc_final: 0.7275 (mmt) REVERT: B 249 MET cc_start: 0.6586 (ttm) cc_final: 0.6341 (mtp) REVERT: B 337 MET cc_start: 0.7944 (ppp) cc_final: 0.5333 (mtt) outliers start: 13 outliers final: 11 residues processed: 117 average time/residue: 0.2297 time to fit residues: 35.7033 Evaluate side-chains 118 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 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 309 THR Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 453 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.0370 chunk 76 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 430 ASN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.189273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.155683 restraints weight = 10148.510| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.75 r_work: 0.3811 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7107 Z= 0.126 Angle : 0.595 9.335 9633 Z= 0.304 Chirality : 0.044 0.167 1051 Planarity : 0.004 0.043 1240 Dihedral : 4.703 52.223 993 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.54 % Allowed : 17.69 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.30), residues: 823 helix: 1.38 (0.28), residues: 356 sheet: -0.16 (0.55), residues: 94 loop : -0.65 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 196 HIS 0.004 0.001 HIS B 329 PHE 0.031 0.002 PHE B 453 TYR 0.029 0.001 TYR A 274 ARG 0.007 0.000 ARG A 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 4) link_NAG-ASN : angle 1.32692 ( 12) hydrogen bonds : bond 0.03150 ( 283) hydrogen bonds : angle 4.37110 ( 822) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.59030 ( 2) covalent geometry : bond 0.00289 ( 7102) covalent geometry : angle 0.59353 ( 9619) ********************** 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 131 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.770 Fit side-chains REVERT: A 145 THR cc_start: 0.7916 (p) cc_final: 0.7599 (m) REVERT: A 212 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7013 (tp) REVERT: A 330 MET cc_start: 0.7116 (ptp) cc_final: 0.6893 (ptp) REVERT: A 452 MET cc_start: 0.7309 (mmm) cc_final: 0.7078 (mmm) REVERT: B 30 MET cc_start: 0.7901 (mmm) cc_final: 0.7266 (mmt) REVERT: B 337 MET cc_start: 0.7941 (ppp) cc_final: 0.5449 (mtt) REVERT: B 393 MET cc_start: 0.7273 (pmm) cc_final: 0.6905 (ptp) outliers start: 12 outliers final: 10 residues processed: 126 average time/residue: 0.3005 time to fit residues: 52.6486 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 : 1.323 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 398 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 0.0060 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** B 260 HIS ** 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 = 0.4325 r_free = 0.4325 target = 0.189895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155860 restraints weight = 10026.240| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.84 r_work: 0.3810 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7107 Z= 0.118 Angle : 0.592 9.451 9633 Z= 0.300 Chirality : 0.044 0.167 1051 Planarity : 0.004 0.044 1240 Dihedral : 4.609 52.139 993 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.41 % Allowed : 17.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.30), residues: 823 helix: 1.43 (0.28), residues: 356 sheet: -0.14 (0.55), residues: 94 loop : -0.64 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 196 HIS 0.003 0.001 HIS B 409 PHE 0.035 0.002 PHE B 453 TYR 0.029 0.001 TYR B 276 ARG 0.007 0.000 ARG A 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 4) link_NAG-ASN : angle 1.33245 ( 12) hydrogen bonds : bond 0.03018 ( 283) hydrogen bonds : angle 4.31364 ( 822) SS BOND : bond 0.00079 ( 1) SS BOND : angle 0.58615 ( 2) covalent geometry : bond 0.00267 ( 7102) covalent geometry : angle 0.59065 ( 9619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3946.90 seconds wall clock time: 72 minutes 4.71 seconds (4324.71 seconds total)