Starting phenix.real_space_refine on Fri Jul 3 14:15:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9der_46794/07_2026/9der_46794_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9der_46794/07_2026/9der_46794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9der_46794/07_2026/9der_46794_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9der_46794/07_2026/9der_46794_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9der_46794/07_2026/9der_46794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9der_46794/07_2026/9der_46794.map" } resolution = 3.9 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= 0.014 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: 7 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 44 5.16 5 C 4612 2.51 5 N 1232 2.21 5 O 1469 1.98 5 H 6843 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14207 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 6697 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 26, 'TRANS': 421} Chain: "B" Number of atoms: 7265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 7265 Classifications: {'peptide': 477} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 449} Chain breaks: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 33 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1, 'water': 2} Link IDs: {None: 2} Chain breaks: 2 Time building chain proxies: 2.26, per 1000 atoms: 0.16 Number of scatterers: 14207 At special positions: 0 Unit cell: (82.08, 101.52, 166.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 6 19.99 S 44 16.00 Mg 1 11.99 O 1469 8.00 N 1232 7.00 C 4612 6.00 H 6843 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 460 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " BMA E 3 " - " BMA E 4 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " BETA1-6 " BMA D 3 " - " BMA D 4 " NAG-ASN " NAG C 1 " - " ASN A 249 " " NAG D 1 " - " ASN B 320 " " NAG E 1 " - " ASN A 15 " " NAG F 1 " - " ASN B 371 " " NAG G 1 " - " ASN B 99 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 302.9 milliseconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1686 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 13 sheets defined 17.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'B' and resid 12 through 19 Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.982A pdb=" N GLY B 34 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 123 through 146 removed outlier: 4.429A pdb=" N ASP B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N SER B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.141A pdb=" N GLU B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 210 Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.799A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.169A pdb=" N ALA B 263 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 287 removed outlier: 4.361A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 303 Processing helix chain 'B' and resid 314 through 325 removed outlier: 3.779A pdb=" N TYR B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.900A pdb=" N LEU B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 441 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 11 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 27 removed outlier: 3.634A pdb=" N SER A 22 " --> pdb=" O GLY A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 100 removed outlier: 3.739A pdb=" N SER A 96 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 242 removed outlier: 6.773A pdb=" N VAL A 267 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG A 279 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 269 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.565A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 65 removed outlier: 6.252A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 197 removed outlier: 6.525A pdb=" N VAL B 193 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ALA B 155 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N THR B 195 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE B 153 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 119 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B 250 " --> pdb=" O ALA B 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 454 through 456 253 hydrogen bonds defined for protein. 660 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: 2.37 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6841 1.03 - 1.23: 16 1.23 - 1.42: 3182 1.42 - 1.62: 4265 1.62 - 1.82: 59 Bond restraints: 14363 Sorted by residual: bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.84e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C1 BMA D 4 " pdb=" C2 BMA D 4 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 BMA E 4 " pdb=" C2 BMA E 4 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.410 1.438 -0.028 2.00e-02 2.50e+03 2.03e+00 ... (remaining 14358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.09: 25789 7.09 - 14.19: 1 14.19 - 21.28: 0 21.28 - 28.37: 0 28.37 - 35.46: 3 Bond angle restraints: 25793 Sorted by residual: angle pdb=" C LYS B 72 " pdb=" CA LYS B 72 " pdb=" HA LYS B 72 " ideal model delta sigma weight residual 109.00 73.54 35.46 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N LYS B 72 " pdb=" CA LYS B 72 " pdb=" HA LYS B 72 " ideal model delta sigma weight residual 110.00 74.64 35.36 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB LYS B 72 " pdb=" CA LYS B 72 " pdb=" HA LYS B 72 " ideal model delta sigma weight residual 109.00 79.83 29.17 3.00e+00 1.11e-01 9.45e+01 angle pdb=" N LYS B 72 " pdb=" CA LYS B 72 " pdb=" C LYS B 72 " ideal model delta sigma weight residual 111.00 121.57 -10.57 2.80e+00 1.28e-01 1.43e+01 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.60 6.35 3.00e+00 1.11e-01 4.48e+00 ... (remaining 25788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 6756 22.77 - 45.53: 230 45.53 - 68.30: 70 68.30 - 91.07: 38 91.07 - 113.84: 24 Dihedral angle restraints: 7118 sinusoidal: 4024 harmonic: 3094 Sorted by residual: dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 38 " pdb=" CB CYS B 38 " ideal model delta sinusoidal sigma weight residual -86.00 -132.89 46.89 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CB CYS B 448 " pdb=" SG CYS B 448 " pdb=" SG CYS B 460 " pdb=" CB CYS B 460 " ideal model delta sinusoidal sigma weight residual 93.00 128.55 -35.55 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 288.71 174.87 113.84 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 7115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1066 0.093 - 0.187: 82 0.187 - 0.280: 7 0.280 - 0.374: 2 0.374 - 0.467: 2 Chirality restraints: 1159 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 249 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA LYS B 72 " pdb=" N LYS B 72 " pdb=" C LYS B 72 " pdb=" CB LYS B 72 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1156 not shown) Planarity restraints: 2194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 380 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO B 381 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 381 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 381 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 93 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO B 94 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 336 " 0.017 5.00e-02 4.00e+02 2.53e-02 1.03e+00 pdb=" N PRO A 337 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.014 5.00e-02 4.00e+02 ... (remaining 2191 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 564 2.17 - 2.78: 27587 2.78 - 3.38: 38070 3.38 - 3.99: 49374 3.99 - 4.60: 76502 Nonbonded interactions: 192097 Sorted by model distance: nonbonded pdb=" O GLN B 267 " pdb=" H ASP B 288 " model vdw 1.560 2.450 nonbonded pdb=" OD1 ASP B 158 " pdb=" H LYS B 159 " model vdw 1.622 2.450 nonbonded pdb=" O GLU B 356 " pdb=" H VAL B 419 " model vdw 1.626 2.450 nonbonded pdb=" H ILE B 256 " pdb=" OD2 ASP B 259 " model vdw 1.627 2.450 nonbonded pdb=" O ASP B 127 " pdb=" HG SER B 130 " model vdw 1.642 2.450 ... (remaining 192092 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 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'E' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.100 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 0.039 7551 Z= 0.135 Angle : 0.589 10.574 10294 Z= 0.248 Chirality : 0.052 0.467 1159 Planarity : 0.003 0.028 1322 Dihedral : 15.299 113.836 3011 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.90 % Allowed : 4.62 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.28), residues: 919 helix: 0.51 (0.51), residues: 126 sheet: 0.95 (0.33), residues: 254 loop : -0.89 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.007 0.001 TYR B 318 PHE 0.008 0.001 PHE B 414 TRP 0.006 0.000 TRP B 466 HIS 0.002 0.000 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 7520) covalent geometry : angle 0.56467 / 0.24 (10216) SS BOND : bond 0.00128 / 0.08 ( 15) SS BOND : angle 0.50332 / 0.32 ( 30) hydrogen bonds : bond 0.17080 / 10.93 ( 253) hydrogen bonds : angle 7.43104 / 5.20 ( 660) link_BETA1-4 : bond 0.00682 / 0.43 ( 10) link_BETA1-4 : angle 2.46635 / 1.71 ( 30) link_BETA1-6 : bond 0.00396 / 0.26 ( 1) link_BETA1-6 : angle 1.29029 / 0.81 ( 3) link_NAG-ASN : bond 0.00611 / 0.35 ( 5) link_NAG-ASN : angle 2.82170 / 1.48 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8725 (tp30) cc_final: 0.8234 (tp30) REVERT: A 49 GLU cc_start: 0.9386 (pt0) cc_final: 0.8927 (pm20) REVERT: A 71 ASP cc_start: 0.8509 (m-30) cc_final: 0.8013 (t0) REVERT: A 420 SER cc_start: 0.9176 (t) cc_final: 0.8892 (p) REVERT: A 435 LEU cc_start: 0.9404 (tp) cc_final: 0.9196 (tp) REVERT: B 131 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8953 (pt) REVERT: B 282 SER cc_start: 0.9329 (m) cc_final: 0.9026 (p) outliers start: 7 outliers final: 3 residues processed: 143 average time/residue: 0.1960 time to fit residues: 35.8078 Evaluate side-chains 88 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.0470 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 333 GLN A 444 GLN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.066746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.052536 restraints weight = 159980.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.054617 restraints weight = 79607.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.056031 restraints weight = 47344.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.057115 restraints weight = 31923.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.057781 restraints weight = 23110.379| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7551 Z= 0.161 Angle : 0.654 10.407 10294 Z= 0.309 Chirality : 0.048 0.452 1159 Planarity : 0.004 0.066 1322 Dihedral : 13.752 84.008 1365 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.41 % Allowed : 9.36 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.28), residues: 919 helix: 0.88 (0.51), residues: 123 sheet: 0.63 (0.32), residues: 261 loop : -0.89 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 320 TYR 0.014 0.001 TYR B 318 PHE 0.025 0.001 PHE B 308 TRP 0.008 0.001 TRP B 129 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 7520) covalent geometry : angle 0.62631 / 0.30 (10216) SS BOND : bond 0.00450 / 0.23 ( 15) SS BOND : angle 0.99232 / 0.61 ( 30) hydrogen bonds : bond 0.04380 / 2.94 ( 253) hydrogen bonds : angle 6.11465 / 4.26 ( 660) link_BETA1-4 : bond 0.00676 / 0.41 ( 10) link_BETA1-4 : angle 2.70450 / 1.90 ( 30) link_BETA1-6 : bond 0.00660 / 0.44 ( 1) link_BETA1-6 : angle 3.76433 / 3.10 ( 3) link_NAG-ASN : bond 0.00452 / 0.29 ( 5) link_NAG-ASN : angle 2.58943 / 1.30 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8718 (tp30) cc_final: 0.8196 (tp30) REVERT: A 49 GLU cc_start: 0.9444 (pt0) cc_final: 0.8847 (pm20) REVERT: A 71 ASP cc_start: 0.8827 (m-30) cc_final: 0.8061 (t0) REVERT: A 127 VAL cc_start: 0.8398 (m) cc_final: 0.7850 (t) REVERT: A 420 SER cc_start: 0.9175 (t) cc_final: 0.8910 (p) REVERT: B 131 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8931 (pt) REVERT: B 282 SER cc_start: 0.9184 (m) cc_final: 0.8820 (p) outliers start: 11 outliers final: 8 residues processed: 88 average time/residue: 0.1905 time to fit residues: 21.8360 Evaluate side-chains 84 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 40 optimal weight: 0.0970 chunk 28 optimal weight: 7.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 82 GLN ** B 215 ASN ** 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 = 0.4019 r_free = 0.4019 target = 0.065419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.051397 restraints weight = 162331.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.053354 restraints weight = 80898.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.054768 restraints weight = 48825.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.055803 restraints weight = 32975.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.056455 restraints weight = 24127.715| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7551 Z= 0.132 Angle : 0.602 10.391 10294 Z= 0.281 Chirality : 0.048 0.451 1159 Planarity : 0.004 0.043 1322 Dihedral : 10.519 80.649 1365 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.28 % Allowed : 10.26 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.28), residues: 919 helix: 0.71 (0.49), residues: 123 sheet: 0.72 (0.34), residues: 241 loop : -1.00 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 165 TYR 0.014 0.001 TYR B 318 PHE 0.017 0.001 PHE B 223 TRP 0.009 0.001 TRP B 129 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 7520) covalent geometry : angle 0.57538 / 0.28 (10216) SS BOND : bond 0.00173 / 0.08 ( 15) SS BOND : angle 0.67547 / 0.40 ( 30) hydrogen bonds : bond 0.03756 / 2.57 ( 253) hydrogen bonds : angle 5.75494 / 4.01 ( 660) link_BETA1-4 : bond 0.00656 / 0.39 ( 10) link_BETA1-4 : angle 2.71640 / 1.90 ( 30) link_BETA1-6 : bond 0.00600 / 0.40 ( 1) link_BETA1-6 : angle 3.00056 / 2.34 ( 3) link_NAG-ASN : bond 0.00437 / 0.27 ( 5) link_NAG-ASN : angle 2.43397 / 1.23 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8732 (tp30) cc_final: 0.8003 (tp30) REVERT: A 49 GLU cc_start: 0.9431 (pt0) cc_final: 0.8842 (pm20) REVERT: A 71 ASP cc_start: 0.8877 (m-30) cc_final: 0.8127 (t0) REVERT: A 420 SER cc_start: 0.9046 (t) cc_final: 0.8792 (p) REVERT: B 282 SER cc_start: 0.9166 (m) cc_final: 0.8778 (p) outliers start: 10 outliers final: 9 residues processed: 81 average time/residue: 0.2087 time to fit residues: 21.6651 Evaluate side-chains 80 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 0.0770 chunk 74 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS ** B 215 ASN ** 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 = 0.3957 r_free = 0.3957 target = 0.063469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.049752 restraints weight = 167229.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.051597 restraints weight = 83764.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.052799 restraints weight = 50097.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.053670 restraints weight = 33760.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.054250 restraints weight = 25113.509| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7551 Z= 0.162 Angle : 0.584 10.306 10294 Z= 0.282 Chirality : 0.045 0.450 1159 Planarity : 0.004 0.064 1322 Dihedral : 8.645 76.813 1365 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.54 % Allowed : 10.77 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.27), residues: 919 helix: 0.82 (0.50), residues: 122 sheet: 0.62 (0.35), residues: 231 loop : -1.15 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 320 TYR 0.016 0.001 TYR B 318 PHE 0.042 0.002 PHE B 223 TRP 0.010 0.001 TRP B 129 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 7520) covalent geometry : angle 0.55949 / 0.28 (10216) SS BOND : bond 0.00161 / 0.09 ( 15) SS BOND : angle 0.66857 / 0.43 ( 30) hydrogen bonds : bond 0.03474 / 2.38 ( 253) hydrogen bonds : angle 5.59216 / 3.89 ( 660) link_BETA1-4 : bond 0.00645 / 0.38 ( 10) link_BETA1-4 : angle 2.61025 / 1.84 ( 30) link_BETA1-6 : bond 0.00487 / 0.32 ( 1) link_BETA1-6 : angle 1.78124 / 1.33 ( 3) link_NAG-ASN : bond 0.00400 / 0.25 ( 5) link_NAG-ASN : angle 2.35801 / 1.19 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.9447 (pt0) cc_final: 0.9173 (pm20) REVERT: A 71 ASP cc_start: 0.8947 (m-30) cc_final: 0.8273 (t0) REVERT: A 235 TRP cc_start: 0.8901 (t60) cc_final: 0.8440 (t60) REVERT: B 266 VAL cc_start: 0.5822 (OUTLIER) cc_final: 0.5411 (p) REVERT: B 282 SER cc_start: 0.9190 (m) cc_final: 0.8815 (p) REVERT: B 295 MET cc_start: 0.8227 (mtt) cc_final: 0.8010 (mtt) outliers start: 12 outliers final: 6 residues processed: 78 average time/residue: 0.1920 time to fit residues: 19.2374 Evaluate side-chains 75 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.063248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.049502 restraints weight = 165423.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.051321 restraints weight = 83197.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.052518 restraints weight = 49797.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.053403 restraints weight = 33660.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.053978 restraints weight = 24574.987| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7551 Z= 0.123 Angle : 0.555 10.422 10294 Z= 0.266 Chirality : 0.045 0.452 1159 Planarity : 0.004 0.040 1322 Dihedral : 8.173 73.021 1364 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.03 % Allowed : 11.92 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.28), residues: 919 helix: 1.05 (0.51), residues: 123 sheet: 0.52 (0.35), residues: 231 loop : -1.13 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 335 TYR 0.026 0.001 TYR A 329 PHE 0.027 0.001 PHE B 223 TRP 0.008 0.001 TRP B 129 HIS 0.013 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 7520) covalent geometry : angle 0.53256 / 0.26 (10216) SS BOND : bond 0.00105 / 0.04 ( 15) SS BOND : angle 0.47908 / 0.30 ( 30) hydrogen bonds : bond 0.03086 / 2.12 ( 253) hydrogen bonds : angle 5.43922 / 3.80 ( 660) link_BETA1-4 : bond 0.00645 / 0.39 ( 10) link_BETA1-4 : angle 2.42286 / 1.73 ( 30) link_BETA1-6 : bond 0.00446 / 0.30 ( 1) link_BETA1-6 : angle 1.53621 / 1.20 ( 3) link_NAG-ASN : bond 0.00465 / 0.28 ( 5) link_NAG-ASN : angle 2.31234 / 1.18 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.9432 (pt0) cc_final: 0.9152 (pm20) REVERT: A 71 ASP cc_start: 0.8953 (m-30) cc_final: 0.8245 (t0) REVERT: A 235 TRP cc_start: 0.8894 (t60) cc_final: 0.8473 (t60) REVERT: B 266 VAL cc_start: 0.6058 (OUTLIER) cc_final: 0.5750 (p) REVERT: B 282 SER cc_start: 0.9188 (m) cc_final: 0.8803 (p) outliers start: 8 outliers final: 6 residues processed: 75 average time/residue: 0.2405 time to fit residues: 23.4317 Evaluate side-chains 74 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 45 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.062826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.049045 restraints weight = 165162.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.050858 restraints weight = 83333.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.052044 restraints weight = 50052.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.052912 restraints weight = 33900.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.053494 restraints weight = 24792.310| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7551 Z= 0.125 Angle : 0.558 10.465 10294 Z= 0.266 Chirality : 0.045 0.453 1159 Planarity : 0.004 0.041 1322 Dihedral : 7.864 68.879 1364 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.15 % Allowed : 11.92 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.28), residues: 919 helix: 1.01 (0.51), residues: 124 sheet: 0.50 (0.35), residues: 231 loop : -1.16 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.014 0.001 TYR B 318 PHE 0.025 0.001 PHE B 223 TRP 0.008 0.001 TRP B 129 HIS 0.007 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 7520) covalent geometry : angle 0.53682 / 0.26 (10216) SS BOND : bond 0.00105 / 0.05 ( 15) SS BOND : angle 0.48853 / 0.32 ( 30) hydrogen bonds : bond 0.03032 / 2.08 ( 253) hydrogen bonds : angle 5.32148 / 3.72 ( 660) link_BETA1-4 : bond 0.00661 / 0.40 ( 10) link_BETA1-4 : angle 2.38825 / 1.72 ( 30) link_BETA1-6 : bond 0.00381 / 0.25 ( 1) link_BETA1-6 : angle 1.48002 / 1.13 ( 3) link_NAG-ASN : bond 0.00440 / 0.27 ( 5) link_NAG-ASN : angle 2.26583 / 1.17 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.9451 (pt0) cc_final: 0.9188 (pm20) REVERT: A 71 ASP cc_start: 0.8953 (m-30) cc_final: 0.8258 (t0) REVERT: A 235 TRP cc_start: 0.8966 (t60) cc_final: 0.8520 (t60) REVERT: B 266 VAL cc_start: 0.6124 (OUTLIER) cc_final: 0.5804 (p) outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.2653 time to fit residues: 24.9076 Evaluate side-chains 74 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 10 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.063260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.049379 restraints weight = 162970.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.051201 restraints weight = 81870.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.052406 restraints weight = 48979.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.053261 restraints weight = 33045.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.053843 restraints weight = 24358.164| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7551 Z= 0.096 Angle : 0.549 10.579 10294 Z= 0.259 Chirality : 0.046 0.455 1159 Planarity : 0.004 0.041 1322 Dihedral : 7.544 64.607 1362 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.64 % Allowed : 12.56 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.28), residues: 919 helix: 1.24 (0.52), residues: 124 sheet: 0.48 (0.35), residues: 233 loop : -1.11 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.012 0.001 TYR A 380 PHE 0.020 0.001 PHE B 308 TRP 0.007 0.001 TRP B 129 HIS 0.008 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 ( 7520) covalent geometry : angle 0.52862 / 0.25 (10216) SS BOND : bond 0.00089 / 0.05 ( 15) SS BOND : angle 0.42265 / 0.27 ( 30) hydrogen bonds : bond 0.02796 / 1.90 ( 253) hydrogen bonds : angle 5.20059 / 3.65 ( 660) link_BETA1-4 : bond 0.00655 / 0.40 ( 10) link_BETA1-4 : angle 2.34731 / 1.70 ( 30) link_BETA1-6 : bond 0.00455 / 0.30 ( 1) link_BETA1-6 : angle 1.38501 / 1.03 ( 3) link_NAG-ASN : bond 0.00503 / 0.30 ( 5) link_NAG-ASN : angle 2.22131 / 1.15 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8833 (tp30) cc_final: 0.8235 (tp30) REVERT: A 49 GLU cc_start: 0.9457 (pt0) cc_final: 0.8964 (pm20) REVERT: A 71 ASP cc_start: 0.8990 (m-30) cc_final: 0.8295 (t0) REVERT: A 235 TRP cc_start: 0.8944 (t60) cc_final: 0.8489 (t60) REVERT: B 142 MET cc_start: 0.9288 (mmm) cc_final: 0.8670 (mmm) REVERT: B 266 VAL cc_start: 0.6414 (OUTLIER) cc_final: 0.6114 (p) outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.2630 time to fit residues: 25.4561 Evaluate side-chains 73 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 87 optimal weight: 30.0000 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.062857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.048918 restraints weight = 163762.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.050713 restraints weight = 82762.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.051910 restraints weight = 49832.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.052749 restraints weight = 33819.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.053327 restraints weight = 24991.316| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7551 Z= 0.106 Angle : 0.548 10.548 10294 Z= 0.261 Chirality : 0.045 0.454 1159 Planarity : 0.004 0.038 1322 Dihedral : 7.359 63.321 1362 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.90 % Allowed : 12.95 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.28), residues: 919 helix: 1.05 (0.51), residues: 124 sheet: 0.45 (0.35), residues: 233 loop : -1.13 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.013 0.001 TYR B 318 PHE 0.019 0.001 PHE B 308 TRP 0.007 0.001 TRP B 129 HIS 0.007 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 7520) covalent geometry : angle 0.52727 / 0.26 (10216) SS BOND : bond 0.00143 / 0.05 ( 15) SS BOND : angle 0.52659 / 0.32 ( 30) hydrogen bonds : bond 0.02770 / 1.89 ( 253) hydrogen bonds : angle 5.18314 / 3.64 ( 660) link_BETA1-4 : bond 0.00642 / 0.40 ( 10) link_BETA1-4 : angle 2.34246 / 1.70 ( 30) link_BETA1-6 : bond 0.00415 / 0.28 ( 1) link_BETA1-6 : angle 1.41235 / 1.07 ( 3) link_NAG-ASN : bond 0.00460 / 0.28 ( 5) link_NAG-ASN : angle 2.21816 / 1.15 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8867 (tp30) cc_final: 0.8279 (tp30) REVERT: A 49 GLU cc_start: 0.9449 (pt0) cc_final: 0.8957 (pm20) REVERT: A 71 ASP cc_start: 0.9011 (m-30) cc_final: 0.8310 (t0) REVERT: A 235 TRP cc_start: 0.8995 (t60) cc_final: 0.8538 (t60) REVERT: B 227 MET cc_start: 0.8213 (tmm) cc_final: 0.7910 (tmm) REVERT: B 266 VAL cc_start: 0.6313 (OUTLIER) cc_final: 0.5990 (p) outliers start: 7 outliers final: 5 residues processed: 76 average time/residue: 0.2430 time to fit residues: 23.7338 Evaluate side-chains 73 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 40 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.062196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.048397 restraints weight = 166530.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.050178 restraints weight = 83722.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.051346 restraints weight = 50192.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.052198 restraints weight = 33933.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.052741 restraints weight = 24902.347| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7551 Z= 0.118 Angle : 0.554 10.537 10294 Z= 0.264 Chirality : 0.045 0.455 1159 Planarity : 0.004 0.038 1322 Dihedral : 7.214 61.311 1362 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.15 % Allowed : 12.95 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.28), residues: 919 helix: 1.20 (0.51), residues: 124 sheet: 0.41 (0.35), residues: 233 loop : -1.15 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.015 0.001 TYR B 318 PHE 0.017 0.001 PHE B 308 TRP 0.007 0.001 TRP B 129 HIS 0.006 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 7520) covalent geometry : angle 0.53396 / 0.26 (10216) SS BOND : bond 0.00108 / 0.04 ( 15) SS BOND : angle 0.49671 / 0.31 ( 30) hydrogen bonds : bond 0.02823 / 1.91 ( 253) hydrogen bonds : angle 5.14819 / 3.62 ( 660) link_BETA1-4 : bond 0.00651 / 0.41 ( 10) link_BETA1-4 : angle 2.32166 / 1.69 ( 30) link_BETA1-6 : bond 0.00389 / 0.26 ( 1) link_BETA1-6 : angle 1.40926 / 1.07 ( 3) link_NAG-ASN : bond 0.00420 / 0.26 ( 5) link_NAG-ASN : angle 2.19301 / 1.15 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8808 (tp30) cc_final: 0.8211 (tp30) REVERT: A 49 GLU cc_start: 0.9453 (pt0) cc_final: 0.9015 (pm20) REVERT: A 71 ASP cc_start: 0.9008 (m-30) cc_final: 0.8284 (t0) REVERT: A 235 TRP cc_start: 0.9042 (t60) cc_final: 0.8585 (t60) REVERT: B 142 MET cc_start: 0.9277 (mmm) cc_final: 0.8658 (mmm) REVERT: B 266 VAL cc_start: 0.6736 (OUTLIER) cc_final: 0.6420 (p) outliers start: 9 outliers final: 6 residues processed: 73 average time/residue: 0.2195 time to fit residues: 20.5996 Evaluate side-chains 71 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 53 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 33 optimal weight: 0.0980 chunk 86 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.062156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.048301 restraints weight = 168668.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.050098 restraints weight = 84855.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.051276 restraints weight = 50789.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.052152 restraints weight = 34409.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.052709 restraints weight = 25247.533| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7551 Z= 0.111 Angle : 0.572 10.593 10294 Z= 0.272 Chirality : 0.046 0.456 1159 Planarity : 0.004 0.038 1322 Dihedral : 7.167 59.649 1362 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.15 % Allowed : 12.95 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.28), residues: 919 helix: 1.11 (0.50), residues: 124 sheet: 0.40 (0.35), residues: 233 loop : -1.14 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 320 TYR 0.013 0.001 TYR B 318 PHE 0.016 0.001 PHE B 308 TRP 0.007 0.001 TRP B 129 HIS 0.006 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7520) covalent geometry : angle 0.54618 / 0.26 (10216) SS BOND : bond 0.00094 / 0.04 ( 15) SS BOND : angle 1.65989 / 1.19 ( 30) hydrogen bonds : bond 0.02713 / 1.85 ( 253) hydrogen bonds : angle 5.12258 / 3.60 ( 660) link_BETA1-4 : bond 0.00589 / 0.38 ( 10) link_BETA1-4 : angle 2.28497 / 1.66 ( 30) link_BETA1-6 : bond 0.00412 / 0.27 ( 1) link_BETA1-6 : angle 1.38626 / 1.04 ( 3) link_NAG-ASN : bond 0.00438 / 0.26 ( 5) link_NAG-ASN : angle 2.16823 / 1.14 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8790 (tp30) cc_final: 0.8201 (tp30) REVERT: A 49 GLU cc_start: 0.9451 (pt0) cc_final: 0.9035 (pm20) REVERT: A 71 ASP cc_start: 0.9037 (m-30) cc_final: 0.8310 (t0) REVERT: A 235 TRP cc_start: 0.9043 (t60) cc_final: 0.8561 (t60) REVERT: B 266 VAL cc_start: 0.6789 (OUTLIER) cc_final: 0.6478 (p) outliers start: 9 outliers final: 8 residues processed: 70 average time/residue: 0.2412 time to fit residues: 21.7651 Evaluate side-chains 72 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 52 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.059760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.045969 restraints weight = 171875.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.047653 restraints weight = 87551.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.048738 restraints weight = 53052.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.049529 restraints weight = 36657.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.050106 restraints weight = 27004.027| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7551 Z= 0.209 Angle : 0.626 10.572 10294 Z= 0.309 Chirality : 0.045 0.458 1159 Planarity : 0.004 0.038 1322 Dihedral : 7.398 58.389 1362 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.03 % Allowed : 12.95 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.27), residues: 919 helix: 0.74 (0.47), residues: 124 sheet: 0.23 (0.35), residues: 233 loop : -1.29 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 320 TYR 0.021 0.002 TYR B 318 PHE 0.014 0.002 PHE B 308 TRP 0.011 0.002 TRP A 100 HIS 0.007 0.002 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 ( 7520) covalent geometry : angle 0.60296 / 0.30 (10216) SS BOND : bond 0.00149 / 0.08 ( 15) SS BOND : angle 1.71498 / 1.23 ( 30) hydrogen bonds : bond 0.03364 / 2.32 ( 253) hydrogen bonds : angle 5.41819 / 3.79 ( 660) link_BETA1-4 : bond 0.00533 / 0.34 ( 10) link_BETA1-4 : angle 2.25065 / 1.64 ( 30) link_BETA1-6 : bond 0.00182 / 0.12 ( 1) link_BETA1-6 : angle 1.54448 / 1.21 ( 3) link_NAG-ASN : bond 0.00313 / 0.19 ( 5) link_NAG-ASN : angle 2.24107 / 1.19 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2507.42 seconds wall clock time: 43 minutes 41.81 seconds (2621.81 seconds total)