Starting phenix.real_space_refine on Thu Jul 2 03:18:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p5j_13200/07_2026/7p5j_13200.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p5j_13200/07_2026/7p5j_13200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p5j_13200/07_2026/7p5j_13200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p5j_13200/07_2026/7p5j_13200.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7p5j_13200/07_2026/7p5j_13200.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p5j_13200/07_2026/7p5j_13200.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p5j_13200/07_2026/7p5j_13200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p5j_13200/07_2026/7p5j_13200.map" } resolution = 4.0 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4034 2.51 5 N 1036 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 6250 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3069 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 17, 'TRANS': 381} Chain breaks: 1 Chain: "B" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3069 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 17, 'TRANS': 381} Chain breaks: 1 Chain: "C" 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 chiralities: 2 Chain: "D" 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 chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.38, per 1000 atoms: 0.22 Number of scatterers: 6250 At special positions: 0 Unit cell: (88.536, 71.61, 134.106, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1156 8.00 N 1036 7.00 C 4034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 385 " distance=2.03 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 370 " 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 D 1 " - " NAG D 2 " NAG-ASN " NAG A 501 " - " ASN A 284 " " NAG A 502 " - " ASN A 355 " " NAG B 501 " - " ASN B 284 " " NAG B 502 " - " ASN B 355 " " NAG C 1 " - " ASN A 130 " " NAG D 1 " - " ASN B 130 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 333.5 milliseconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 removed outlier: 3.604A pdb=" N HIS A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 70 removed outlier: 3.591A pdb=" N GLN A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 161 Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 198 through 238 removed outlier: 3.636A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 276 removed outlier: 4.116A pdb=" N VAL A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N MET A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 290 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.755A pdb=" N LEU A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 335 removed outlier: 3.759A pdb=" N ARG A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.805A pdb=" N GLN A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 368 removed outlier: 3.565A pdb=" N LYS A 345 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Proline residue: A 346 - end of helix removed outlier: 4.183A pdb=" N SER A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 386 removed outlier: 4.266A pdb=" N LEU A 373 " --> pdb=" O HIS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 418 Proline residue: A 414 - end of helix removed outlier: 4.580A pdb=" N ALA A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 18 Processing helix chain 'B' and resid 37 through 70 removed outlier: 3.620A pdb=" N ALA B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 161 Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.694A pdb=" N ALA B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 238 removed outlier: 3.757A pdb=" N VAL B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 205 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 275 removed outlier: 4.010A pdb=" N VAL B 248 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 290 Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 311 through 335 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.925A pdb=" N GLN B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 368 Processing helix chain 'B' and resid 369 through 385 removed outlier: 4.120A pdb=" N LEU B 373 " --> pdb=" O HIS B 369 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 418 Proline residue: B 414 - end of helix removed outlier: 4.576A pdb=" N ALA B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1975 1.34 - 1.46: 1103 1.46 - 1.58: 3270 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 6378 Sorted by residual: bond pdb=" N ILE B 244 " pdb=" CA ILE B 244 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" CA PRO A 421 " pdb=" C PRO A 421 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 9.10e+00 bond pdb=" N VAL B 243 " pdb=" CA VAL B 243 " ideal model delta sigma weight residual 1.463 1.495 -0.032 1.14e-02 7.69e+03 8.03e+00 bond pdb=" N ASP B 137 " pdb=" CA ASP B 137 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.79e+00 bond pdb=" N LEU B 242 " pdb=" CA LEU B 242 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.16e-02 7.43e+03 6.65e+00 ... (remaining 6373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 8296 1.50 - 3.00: 297 3.00 - 4.50: 77 4.50 - 6.00: 29 6.00 - 7.51: 5 Bond angle restraints: 8704 Sorted by residual: angle pdb=" N PRO A 421 " pdb=" CA PRO A 421 " pdb=" C PRO A 421 " ideal model delta sigma weight residual 110.70 116.89 -6.19 1.22e+00 6.72e-01 2.57e+01 angle pdb=" CA PRO B 421 " pdb=" C PRO B 421 " pdb=" N PRO B 422 " ideal model delta sigma weight residual 117.93 123.81 -5.88 1.20e+00 6.94e-01 2.40e+01 angle pdb=" CA PRO A 421 " pdb=" C PRO A 421 " pdb=" N PRO A 422 " ideal model delta sigma weight residual 117.93 123.57 -5.64 1.20e+00 6.94e-01 2.21e+01 angle pdb=" O PRO B 421 " pdb=" C PRO B 421 " pdb=" N PRO B 422 " ideal model delta sigma weight residual 121.46 116.44 5.02 1.18e+00 7.18e-01 1.81e+01 angle pdb=" CA ASP B 137 " pdb=" CB ASP B 137 " pdb=" CG ASP B 137 " ideal model delta sigma weight residual 112.60 116.68 -4.08 1.00e+00 1.00e+00 1.67e+01 ... (remaining 8699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 3306 17.82 - 35.64: 327 35.64 - 53.46: 75 53.46 - 71.27: 16 71.27 - 89.09: 8 Dihedral angle restraints: 3732 sinusoidal: 1422 harmonic: 2310 Sorted by residual: dihedral pdb=" CB CYS B 303 " pdb=" SG CYS B 303 " pdb=" SG CYS B 370 " pdb=" CB CYS B 370 " ideal model delta sinusoidal sigma weight residual 93.00 9.23 83.77 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CA ASP B 279 " pdb=" C ASP B 279 " pdb=" N PRO B 280 " pdb=" CA PRO B 280 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CB GLU B 204 " pdb=" CG GLU B 204 " pdb=" CD GLU B 204 " pdb=" OE1 GLU B 204 " ideal model delta sinusoidal sigma weight residual 0.00 89.09 -89.09 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 3729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 930 0.061 - 0.122: 131 0.122 - 0.182: 8 0.182 - 0.243: 2 0.243 - 0.304: 1 Chirality restraints: 1072 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.39e+02 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 130 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 130 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1069 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.295 2.00e-02 2.50e+03 2.56e-01 8.19e+02 pdb=" C7 NAG D 2 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.454 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.266 2.00e-02 2.50e+03 2.21e-01 6.13e+02 pdb=" C7 NAG D 1 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.368 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 130 " -0.025 2.00e-02 2.50e+03 2.36e-02 6.95e+00 pdb=" CG ASN A 130 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 130 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 130 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.022 2.00e-02 2.50e+03 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1361 2.79 - 3.32: 6914 3.32 - 3.85: 10669 3.85 - 4.37: 11531 4.37 - 4.90: 19376 Nonbonded interactions: 49851 Sorted by model distance: nonbonded pdb=" O GLU B 154 " pdb=" OG1 THR B 157 " model vdw 2.264 3.040 nonbonded pdb=" O GLU A 154 " pdb=" OG1 THR A 157 " model vdw 2.274 3.040 nonbonded pdb=" O VAL A 90 " pdb=" OG SER A 93 " model vdw 2.286 3.040 nonbonded pdb=" O3 NAG C 1 " pdb=" O7 NAG C 2 " model vdw 2.330 3.040 nonbonded pdb=" OD1 ASN A 205 " pdb=" N VAL A 206 " model vdw 2.344 3.120 ... (remaining 49846 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.800 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.004 0.051 6390 Z= 0.242 Angle : 0.743 8.578 8736 Z= 0.408 Chirality : 0.043 0.304 1072 Planarity : 0.011 0.256 1086 Dihedral : 15.496 89.092 2224 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.60 % Allowed : 1.51 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.31), residues: 790 helix: 2.36 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.51 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 314 TYR 0.026 0.002 TYR A 299 PHE 0.029 0.002 PHE B 208 TRP 0.016 0.001 TRP A 258 HIS 0.004 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.24 ( 6378) covalent geometry : angle 0.72498 / 0.40 ( 8704) SS BOND : bond 0.00192 / 0.10 ( 4) SS BOND : angle 0.65457 / 0.50 ( 8) hydrogen bonds : bond 0.10764 / 7.08 ( 552) hydrogen bonds : angle 5.18823 / 3.87 ( 1656) link_BETA1-4 : bond 0.02207 / 1.50 ( 2) link_BETA1-4 : angle 4.68117 / 3.19 ( 6) link_NAG-ASN : bond 0.01937 / 1.02 ( 6) link_NAG-ASN : angle 2.57245 / 1.89 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 239 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 273 ASP cc_start: 0.7621 (t70) cc_final: 0.6956 (t70) REVERT: A 350 LEU cc_start: 0.8933 (mt) cc_final: 0.8660 (mt) REVERT: B 24 PHE cc_start: 0.7468 (p90) cc_final: 0.7260 (p90) REVERT: B 40 TYR cc_start: 0.7595 (t80) cc_final: 0.7383 (t80) REVERT: B 98 LEU cc_start: 0.8265 (mm) cc_final: 0.8063 (mm) REVERT: B 134 SER cc_start: 0.8916 (m) cc_final: 0.8442 (t) REVERT: B 160 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8682 (tm-30) REVERT: B 167 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7288 (tp30) REVERT: B 304 ASN cc_start: 0.8119 (m-40) cc_final: 0.7624 (m-40) outliers start: 4 outliers final: 2 residues processed: 241 average time/residue: 0.0552 time to fit residues: 18.8085 Evaluate side-chains 203 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 244 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.155766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.134798 restraints weight = 10105.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138193 restraints weight = 5942.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.140411 restraints weight = 4086.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142117 restraints weight = 3132.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142995 restraints weight = 2564.976| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6390 Z= 0.160 Angle : 0.700 9.798 8736 Z= 0.328 Chirality : 0.043 0.283 1072 Planarity : 0.005 0.073 1086 Dihedral : 4.464 52.725 856 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.11 % Allowed : 14.65 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.30), residues: 790 helix: 2.68 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.41 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.020 0.002 TYR A 377 PHE 0.033 0.002 PHE A 208 TRP 0.017 0.001 TRP B 258 HIS 0.005 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 6378) covalent geometry : angle 0.69124 / 0.33 ( 8704) SS BOND : bond 0.00323 / 0.22 ( 4) SS BOND : angle 1.03159 / 0.58 ( 8) hydrogen bonds : bond 0.04457 / 2.89 ( 552) hydrogen bonds : angle 4.24169 / 3.19 ( 1656) link_BETA1-4 : bond 0.01500 / 1.02 ( 2) link_BETA1-4 : angle 3.54895 / 2.15 ( 6) link_NAG-ASN : bond 0.00387 / 0.25 ( 6) link_NAG-ASN : angle 1.35563 / 0.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 217 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8334 (mp) REVERT: A 131 HIS cc_start: 0.8192 (t70) cc_final: 0.7950 (t70) REVERT: A 273 ASP cc_start: 0.7600 (t70) cc_final: 0.7272 (t70) REVERT: B 134 SER cc_start: 0.9063 (m) cc_final: 0.8295 (t) REVERT: B 304 ASN cc_start: 0.8179 (m-40) cc_final: 0.7693 (m-40) REVERT: B 381 LEU cc_start: 0.8373 (mt) cc_final: 0.8166 (mp) outliers start: 14 outliers final: 9 residues processed: 221 average time/residue: 0.0555 time to fit residues: 17.4883 Evaluate side-chains 214 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 347 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 128 HIS B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.154792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.134965 restraints weight = 10126.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137771 restraints weight = 6478.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139859 restraints weight = 4684.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.141172 restraints weight = 3679.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141944 restraints weight = 3107.939| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6390 Z= 0.152 Angle : 0.692 10.195 8736 Z= 0.322 Chirality : 0.041 0.256 1072 Planarity : 0.005 0.064 1086 Dihedral : 3.697 18.169 850 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.27 % Allowed : 18.28 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.30), residues: 790 helix: 2.70 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.24 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.023 0.002 TYR A 299 PHE 0.034 0.002 PHE B 208 TRP 0.018 0.001 TRP B 258 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 6378) covalent geometry : angle 0.68471 / 0.32 ( 8704) SS BOND : bond 0.00276 / 0.16 ( 4) SS BOND : angle 1.07743 / 0.57 ( 8) hydrogen bonds : bond 0.04100 / 2.65 ( 552) hydrogen bonds : angle 4.12493 / 3.11 ( 1656) link_BETA1-4 : bond 0.01851 / 1.28 ( 2) link_BETA1-4 : angle 3.34338 / 1.99 ( 6) link_NAG-ASN : bond 0.00375 / 0.23 ( 6) link_NAG-ASN : angle 1.11989 / 0.69 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 ASP cc_start: 0.7660 (t70) cc_final: 0.7337 (t70) REVERT: A 402 SER cc_start: 0.8817 (p) cc_final: 0.8336 (t) REVERT: B 134 SER cc_start: 0.9101 (m) cc_final: 0.8287 (t) REVERT: B 214 TRP cc_start: 0.6821 (t60) cc_final: 0.6511 (t60) REVERT: B 304 ASN cc_start: 0.8192 (m-40) cc_final: 0.7737 (m-40) REVERT: B 381 LEU cc_start: 0.8465 (mt) cc_final: 0.8104 (mt) REVERT: B 402 SER cc_start: 0.8714 (p) cc_final: 0.8240 (t) outliers start: 15 outliers final: 11 residues processed: 218 average time/residue: 0.0613 time to fit residues: 18.6814 Evaluate side-chains 214 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 41 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS B 128 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.134942 restraints weight = 10029.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.138394 restraints weight = 6016.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140836 restraints weight = 4179.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142470 restraints weight = 3167.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143519 restraints weight = 2589.575| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6390 Z= 0.148 Angle : 0.682 10.113 8736 Z= 0.315 Chirality : 0.042 0.248 1072 Planarity : 0.005 0.061 1086 Dihedral : 3.676 17.906 850 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.87 % Allowed : 19.34 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.30), residues: 790 helix: 2.71 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.40 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.026 0.002 TYR A 299 PHE 0.028 0.002 PHE B 208 TRP 0.019 0.001 TRP B 258 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 6378) covalent geometry : angle 0.67449 / 0.31 ( 8704) SS BOND : bond 0.00453 / 0.30 ( 4) SS BOND : angle 1.18386 / 0.66 ( 8) hydrogen bonds : bond 0.03944 / 2.54 ( 552) hydrogen bonds : angle 4.04174 / 3.06 ( 1656) link_BETA1-4 : bond 0.01818 / 1.25 ( 2) link_BETA1-4 : angle 3.47167 / 2.10 ( 6) link_NAG-ASN : bond 0.00347 / 0.21 ( 6) link_NAG-ASN : angle 1.15304 / 0.68 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 246 MET cc_start: 0.6726 (ppp) cc_final: 0.6402 (ptt) REVERT: A 273 ASP cc_start: 0.7642 (t70) cc_final: 0.7306 (t70) REVERT: A 402 SER cc_start: 0.8738 (p) cc_final: 0.8225 (t) REVERT: B 134 SER cc_start: 0.9128 (m) cc_final: 0.8244 (t) REVERT: B 304 ASN cc_start: 0.8283 (m-40) cc_final: 0.7837 (t0) REVERT: B 309 ASN cc_start: 0.8729 (t0) cc_final: 0.8497 (t0) REVERT: B 381 LEU cc_start: 0.8583 (mt) cc_final: 0.8193 (mt) REVERT: B 402 SER cc_start: 0.8674 (p) cc_final: 0.8155 (t) outliers start: 19 outliers final: 16 residues processed: 216 average time/residue: 0.0607 time to fit residues: 18.5053 Evaluate side-chains 220 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.154834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.133482 restraints weight = 10239.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136995 restraints weight = 6140.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139273 restraints weight = 4253.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.141042 restraints weight = 3270.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142086 restraints weight = 2670.620| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6390 Z= 0.153 Angle : 0.701 11.541 8736 Z= 0.319 Chirality : 0.041 0.256 1072 Planarity : 0.005 0.059 1086 Dihedral : 3.700 17.847 850 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.08 % Allowed : 20.09 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.27 (0.30), residues: 790 helix: 2.77 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -1.38 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 213 TYR 0.027 0.002 TYR A 299 PHE 0.033 0.002 PHE B 208 TRP 0.023 0.001 TRP B 258 HIS 0.009 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 6378) covalent geometry : angle 0.69350 / 0.32 ( 8704) SS BOND : bond 0.00346 / 0.20 ( 4) SS BOND : angle 1.29004 / 0.74 ( 8) hydrogen bonds : bond 0.03852 / 2.47 ( 552) hydrogen bonds : angle 4.03790 / 3.05 ( 1656) link_BETA1-4 : bond 0.01765 / 1.21 ( 2) link_BETA1-4 : angle 3.48866 / 2.12 ( 6) link_NAG-ASN : bond 0.00325 / 0.19 ( 6) link_NAG-ASN : angle 1.16706 / 0.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.7903 (t80) cc_final: 0.7389 (t80) REVERT: A 61 PHE cc_start: 0.7352 (m-80) cc_final: 0.7088 (m-80) REVERT: A 273 ASP cc_start: 0.7701 (t70) cc_final: 0.7293 (t70) REVERT: A 330 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8670 (mt) REVERT: A 402 SER cc_start: 0.8713 (p) cc_final: 0.8186 (t) REVERT: B 134 SER cc_start: 0.9134 (m) cc_final: 0.8206 (t) REVERT: B 246 MET cc_start: 0.7363 (ppp) cc_final: 0.6191 (ppp) REVERT: B 304 ASN cc_start: 0.8226 (m-40) cc_final: 0.7887 (t0) REVERT: B 309 ASN cc_start: 0.8736 (t0) cc_final: 0.8501 (t0) REVERT: B 381 LEU cc_start: 0.8517 (mt) cc_final: 0.8030 (mt) REVERT: B 402 SER cc_start: 0.8656 (p) cc_final: 0.8075 (t) outliers start: 27 outliers final: 23 residues processed: 228 average time/residue: 0.0591 time to fit residues: 18.8702 Evaluate side-chains 227 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 392 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.156257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.134882 restraints weight = 10134.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.138415 restraints weight = 6086.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140758 restraints weight = 4218.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142445 restraints weight = 3246.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143488 restraints weight = 2663.245| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6390 Z= 0.136 Angle : 0.713 14.475 8736 Z= 0.323 Chirality : 0.042 0.235 1072 Planarity : 0.005 0.052 1086 Dihedral : 3.735 17.595 850 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.78 % Allowed : 22.66 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.26 (0.30), residues: 790 helix: 2.78 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -1.44 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 382 TYR 0.027 0.002 TYR A 299 PHE 0.033 0.002 PHE B 208 TRP 0.025 0.001 TRP B 258 HIS 0.016 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 6378) covalent geometry : angle 0.70522 / 0.32 ( 8704) SS BOND : bond 0.00291 / 0.20 ( 4) SS BOND : angle 1.32846 / 0.81 ( 8) hydrogen bonds : bond 0.03783 / 2.43 ( 552) hydrogen bonds : angle 3.99317 / 3.02 ( 1656) link_BETA1-4 : bond 0.01786 / 1.23 ( 2) link_BETA1-4 : angle 3.58323 / 2.21 ( 6) link_NAG-ASN : bond 0.00356 / 0.22 ( 6) link_NAG-ASN : angle 1.17370 / 0.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.7871 (t80) cc_final: 0.7389 (t80) REVERT: A 61 PHE cc_start: 0.7275 (m-80) cc_final: 0.7000 (m-80) REVERT: A 273 ASP cc_start: 0.7750 (t70) cc_final: 0.7354 (t70) REVERT: A 330 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8621 (mt) REVERT: A 402 SER cc_start: 0.8664 (p) cc_final: 0.8178 (t) REVERT: B 134 SER cc_start: 0.9136 (m) cc_final: 0.8056 (t) REVERT: B 246 MET cc_start: 0.7323 (ppp) cc_final: 0.5891 (ppp) REVERT: B 304 ASN cc_start: 0.8221 (m-40) cc_final: 0.7851 (t0) REVERT: B 381 LEU cc_start: 0.8494 (mt) cc_final: 0.7974 (mt) REVERT: B 402 SER cc_start: 0.8654 (p) cc_final: 0.8072 (t) outliers start: 25 outliers final: 22 residues processed: 223 average time/residue: 0.0548 time to fit residues: 17.5197 Evaluate side-chains 228 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 392 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.154741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133565 restraints weight = 10104.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136973 restraints weight = 6060.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139397 restraints weight = 4194.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140971 restraints weight = 3220.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142145 restraints weight = 2653.812| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6390 Z= 0.157 Angle : 0.740 14.225 8736 Z= 0.335 Chirality : 0.043 0.249 1072 Planarity : 0.005 0.054 1086 Dihedral : 3.721 17.660 850 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.78 % Allowed : 24.62 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.30), residues: 790 helix: 2.77 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.54 (0.55), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 382 TYR 0.027 0.002 TYR A 299 PHE 0.031 0.002 PHE B 208 TRP 0.026 0.002 TRP B 258 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 6378) covalent geometry : angle 0.73259 / 0.33 ( 8704) SS BOND : bond 0.00251 / 0.14 ( 4) SS BOND : angle 1.30312 / 0.79 ( 8) hydrogen bonds : bond 0.03821 / 2.47 ( 552) hydrogen bonds : angle 4.04836 / 3.07 ( 1656) link_BETA1-4 : bond 0.01715 / 1.18 ( 2) link_BETA1-4 : angle 3.59184 / 2.20 ( 6) link_NAG-ASN : bond 0.00344 / 0.21 ( 6) link_NAG-ASN : angle 1.16827 / 0.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.7830 (t80) cc_final: 0.7265 (t80) REVERT: A 61 PHE cc_start: 0.7034 (m-80) cc_final: 0.6779 (m-80) REVERT: A 95 ILE cc_start: 0.8100 (mp) cc_final: 0.7877 (mm) REVERT: A 114 GLU cc_start: 0.8669 (tp30) cc_final: 0.8355 (tp30) REVERT: A 273 ASP cc_start: 0.7659 (t70) cc_final: 0.7304 (t70) REVERT: A 330 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8639 (mt) REVERT: A 402 SER cc_start: 0.8682 (p) cc_final: 0.8189 (t) REVERT: B 134 SER cc_start: 0.9140 (m) cc_final: 0.8210 (t) REVERT: B 246 MET cc_start: 0.7143 (ppp) cc_final: 0.5774 (ppp) REVERT: B 304 ASN cc_start: 0.8216 (m-40) cc_final: 0.7864 (t0) REVERT: B 309 ASN cc_start: 0.8502 (t0) cc_final: 0.8194 (t0) REVERT: B 381 LEU cc_start: 0.8543 (mt) cc_final: 0.7988 (mt) REVERT: B 402 SER cc_start: 0.8676 (p) cc_final: 0.8078 (t) outliers start: 25 outliers final: 20 residues processed: 223 average time/residue: 0.0532 time to fit residues: 17.1980 Evaluate side-chains 228 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 392 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN B 138 HIS B 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.155578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134340 restraints weight = 10162.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137750 restraints weight = 6070.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140193 restraints weight = 4194.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141750 restraints weight = 3207.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142920 restraints weight = 2646.695| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6390 Z= 0.150 Angle : 0.749 14.592 8736 Z= 0.339 Chirality : 0.043 0.254 1072 Planarity : 0.005 0.052 1086 Dihedral : 3.738 17.642 850 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.38 % Allowed : 24.77 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.30), residues: 790 helix: 2.73 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -1.32 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 382 TYR 0.014 0.001 TYR A 299 PHE 0.031 0.002 PHE B 208 TRP 0.025 0.001 TRP B 258 HIS 0.011 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6378) covalent geometry : angle 0.74122 / 0.34 ( 8704) SS BOND : bond 0.00320 / 0.21 ( 4) SS BOND : angle 1.45889 / 0.98 ( 8) hydrogen bonds : bond 0.03790 / 2.44 ( 552) hydrogen bonds : angle 4.02079 / 3.04 ( 1656) link_BETA1-4 : bond 0.01626 / 1.12 ( 2) link_BETA1-4 : angle 3.65769 / 2.28 ( 6) link_NAG-ASN : bond 0.00369 / 0.22 ( 6) link_NAG-ASN : angle 1.12824 / 0.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.7893 (t80) cc_final: 0.7385 (t80) REVERT: A 61 PHE cc_start: 0.7002 (m-80) cc_final: 0.6758 (m-80) REVERT: A 114 GLU cc_start: 0.8635 (tp30) cc_final: 0.8337 (tp30) REVERT: A 273 ASP cc_start: 0.7674 (t70) cc_final: 0.7186 (t70) REVERT: A 330 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8663 (mt) REVERT: A 402 SER cc_start: 0.8695 (p) cc_final: 0.8163 (t) REVERT: B 134 SER cc_start: 0.9103 (m) cc_final: 0.8171 (t) REVERT: B 246 MET cc_start: 0.7165 (ppp) cc_final: 0.5752 (ppp) REVERT: B 304 ASN cc_start: 0.8201 (m-40) cc_final: 0.7862 (t0) REVERT: B 309 ASN cc_start: 0.8496 (t0) cc_final: 0.8159 (t0) REVERT: B 381 LEU cc_start: 0.8528 (mt) cc_final: 0.7972 (mt) REVERT: B 402 SER cc_start: 0.8705 (p) cc_final: 0.8062 (t) outliers start: 29 outliers final: 24 residues processed: 218 average time/residue: 0.0572 time to fit residues: 17.9509 Evaluate side-chains 227 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 392 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 360 ASN B 138 HIS B 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134998 restraints weight = 10127.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137905 restraints weight = 6440.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140023 restraints weight = 4653.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141307 restraints weight = 3651.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142300 restraints weight = 3092.454| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 6390 Z= 0.167 Angle : 0.774 15.180 8736 Z= 0.352 Chirality : 0.044 0.288 1072 Planarity : 0.005 0.059 1086 Dihedral : 3.761 17.664 850 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.53 % Allowed : 24.47 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.30), residues: 790 helix: 2.68 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -1.22 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 382 TYR 0.016 0.002 TYR A 299 PHE 0.029 0.002 PHE B 208 TRP 0.024 0.002 TRP B 258 HIS 0.011 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 6378) covalent geometry : angle 0.76577 / 0.35 ( 8704) SS BOND : bond 0.00354 / 0.22 ( 4) SS BOND : angle 1.68152 / 1.05 ( 8) hydrogen bonds : bond 0.03843 / 2.46 ( 552) hydrogen bonds : angle 4.09488 / 3.11 ( 1656) link_BETA1-4 : bond 0.01680 / 1.15 ( 2) link_BETA1-4 : angle 3.68543 / 2.29 ( 6) link_NAG-ASN : bond 0.00347 / 0.21 ( 6) link_NAG-ASN : angle 1.11337 / 0.61 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8022 (t80) cc_final: 0.7420 (t80) REVERT: A 61 PHE cc_start: 0.7132 (m-80) cc_final: 0.6882 (m-80) REVERT: A 114 GLU cc_start: 0.8722 (tp30) cc_final: 0.8395 (tp30) REVERT: A 273 ASP cc_start: 0.7808 (t70) cc_final: 0.7265 (t70) REVERT: A 330 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8641 (mt) REVERT: A 402 SER cc_start: 0.8688 (p) cc_final: 0.8233 (t) REVERT: B 134 SER cc_start: 0.9156 (m) cc_final: 0.8186 (t) REVERT: B 246 MET cc_start: 0.7301 (ppp) cc_final: 0.6031 (ppp) REVERT: B 304 ASN cc_start: 0.8262 (m-40) cc_final: 0.7875 (t0) REVERT: B 309 ASN cc_start: 0.8554 (t0) cc_final: 0.8171 (t0) REVERT: B 381 LEU cc_start: 0.8485 (mt) cc_final: 0.7936 (mt) REVERT: B 402 SER cc_start: 0.8723 (p) cc_final: 0.8127 (t) outliers start: 30 outliers final: 26 residues processed: 216 average time/residue: 0.0526 time to fit residues: 16.4064 Evaluate side-chains 233 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN B 138 HIS B 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.155931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.134747 restraints weight = 10087.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138287 restraints weight = 6021.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140741 restraints weight = 4137.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142285 restraints weight = 3140.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143472 restraints weight = 2585.537| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6390 Z= 0.146 Angle : 0.772 15.179 8736 Z= 0.347 Chirality : 0.044 0.300 1072 Planarity : 0.005 0.058 1086 Dihedral : 3.774 17.610 850 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.93 % Allowed : 25.08 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.30), residues: 790 helix: 2.67 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -1.10 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 382 TYR 0.015 0.001 TYR A 299 PHE 0.030 0.001 PHE B 208 TRP 0.024 0.001 TRP B 258 HIS 0.016 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 6378) covalent geometry : angle 0.76384 / 0.35 ( 8704) SS BOND : bond 0.00291 / 0.19 ( 4) SS BOND : angle 1.72042 / 1.12 ( 8) hydrogen bonds : bond 0.03783 / 2.44 ( 552) hydrogen bonds : angle 4.04045 / 3.06 ( 1656) link_BETA1-4 : bond 0.01700 / 1.17 ( 2) link_BETA1-4 : angle 3.74682 / 2.36 ( 6) link_NAG-ASN : bond 0.00376 / 0.23 ( 6) link_NAG-ASN : angle 1.11511 / 0.61 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.7906 (t80) cc_final: 0.7371 (t80) REVERT: A 61 PHE cc_start: 0.7027 (m-80) cc_final: 0.6786 (m-80) REVERT: A 114 GLU cc_start: 0.8644 (tp30) cc_final: 0.8337 (tp30) REVERT: A 273 ASP cc_start: 0.7761 (t70) cc_final: 0.7252 (t70) REVERT: A 330 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8695 (mt) REVERT: A 402 SER cc_start: 0.8681 (p) cc_final: 0.8166 (t) REVERT: B 134 SER cc_start: 0.9099 (m) cc_final: 0.8063 (t) REVERT: B 246 MET cc_start: 0.7078 (ppp) cc_final: 0.5782 (ppp) REVERT: B 304 ASN cc_start: 0.8223 (m-40) cc_final: 0.7869 (t0) REVERT: B 309 ASN cc_start: 0.8521 (t0) cc_final: 0.8101 (t0) REVERT: B 381 LEU cc_start: 0.8488 (mt) cc_final: 0.7964 (mt) REVERT: B 402 SER cc_start: 0.8698 (p) cc_final: 0.8041 (t) outliers start: 26 outliers final: 23 residues processed: 218 average time/residue: 0.0568 time to fit residues: 17.5668 Evaluate side-chains 229 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS B 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.155305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134224 restraints weight = 10084.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137724 restraints weight = 6005.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140021 restraints weight = 4141.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141715 restraints weight = 3170.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142391 restraints weight = 2600.305| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6390 Z= 0.153 Angle : 0.781 15.305 8736 Z= 0.352 Chirality : 0.043 0.247 1072 Planarity : 0.005 0.058 1086 Dihedral : 3.752 17.592 850 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.63 % Allowed : 25.38 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.30), residues: 790 helix: 2.70 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -1.18 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 177 TYR 0.015 0.002 TYR A 299 PHE 0.029 0.002 PHE B 208 TRP 0.024 0.002 TRP B 258 HIS 0.018 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 6378) covalent geometry : angle 0.77293 / 0.35 ( 8704) SS BOND : bond 0.00296 / 0.18 ( 4) SS BOND : angle 1.67617 / 1.11 ( 8) hydrogen bonds : bond 0.03795 / 2.45 ( 552) hydrogen bonds : angle 4.05111 / 3.07 ( 1656) link_BETA1-4 : bond 0.01678 / 1.15 ( 2) link_BETA1-4 : angle 3.76213 / 2.36 ( 6) link_NAG-ASN : bond 0.00371 / 0.23 ( 6) link_NAG-ASN : angle 1.12527 / 0.62 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1045.01 seconds wall clock time: 18 minutes 51.40 seconds (1131.40 seconds total)