Starting phenix.real_space_refine on Wed Jul 23 16:46:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7knu_22963/07_2025/7knu_22963.cif Found real_map, /net/cci-nas-00/data/ceres_data/7knu_22963/07_2025/7knu_22963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7knu_22963/07_2025/7knu_22963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7knu_22963/07_2025/7knu_22963.map" model { file = "/net/cci-nas-00/data/ceres_data/7knu_22963/07_2025/7knu_22963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7knu_22963/07_2025/7knu_22963.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 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 31 5.16 5 C 2504 2.51 5 N 631 2.21 5 O 643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3809 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 931 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 108} Chain: "P" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "R" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2796 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 9, 'TRANS': 331} Chain breaks: 4 Time building chain proxies: 2.98, per 1000 atoms: 0.78 Number of scatterers: 3809 At special positions: 0 Unit cell: (63.08, 105.41, 82.17, 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 31 16.00 O 643 8.00 N 631 7.00 C 2504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " 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 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 439.5 milliseconds 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 890 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 68.3% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'E' and resid 29 through 35 removed outlier: 3.547A pdb=" N LEU E 35 " --> pdb=" O ASN E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 50 removed outlier: 3.676A pdb=" N GLN E 45 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 80 removed outlier: 5.458A pdb=" N ARG E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 101 removed outlier: 3.759A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 143 removed outlier: 4.031A pdb=" N PHE E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 3.911A pdb=" N LEU E 131 " --> pdb=" O ILE E 127 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 143 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 54 removed outlier: 4.082A pdb=" N ALA R 44 " --> pdb=" O LYS R 40 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR R 49 " --> pdb=" O GLN R 45 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN R 50 " --> pdb=" O TYR R 46 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 167 removed outlier: 3.719A pdb=" N PHE R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE R 147 " --> pdb=" O TYR R 143 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE R 153 " --> pdb=" O HIS R 149 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA R 154 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER R 159 " --> pdb=" O SER R 155 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE R 162 " --> pdb=" O ILE R 158 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE R 163 " --> pdb=" O SER R 159 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 166 " --> pdb=" O ILE R 162 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS R 167 " --> pdb=" O PHE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 192 removed outlier: 4.146A pdb=" N ASN R 179 " --> pdb=" O THR R 175 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE R 182 " --> pdb=" O LYS R 178 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE R 192 " --> pdb=" O SER R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 208 Processing helix chain 'R' and resid 209 through 242 removed outlier: 3.678A pdb=" N LYS R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY R 224 " --> pdb=" O LEU R 220 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET R 230 " --> pdb=" O ASN R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 261 Processing helix chain 'R' and resid 263 through 278 removed outlier: 3.734A pdb=" N SER R 275 " --> pdb=" O ALA R 271 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR R 277 " --> pdb=" O ALA R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 removed outlier: 3.535A pdb=" N TRP R 283 " --> pdb=" O ASP R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 319 Proline residue: R 297 - end of helix removed outlier: 3.505A pdb=" N LEU R 306 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN R 311 " --> pdb=" O PHE R 307 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE R 317 " --> pdb=" O VAL R 313 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR R 318 " --> pdb=" O ARG R 314 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS R 319 " --> pdb=" O VAL R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 351 removed outlier: 3.668A pdb=" N VAL R 335 " --> pdb=" O TYR R 331 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA R 337 " --> pdb=" O LYS R 333 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU R 341 " --> pdb=" O ALA R 337 " (cutoff:3.500A) Proline residue: R 343 - end of helix removed outlier: 5.650A pdb=" N GLU R 348 " --> pdb=" O LEU R 344 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE R 349 " --> pdb=" O LEU R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 375 removed outlier: 3.596A pdb=" N HIS R 374 " --> pdb=" O HIS R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 385 Processing helix chain 'R' and resid 388 through 402 Processing sheet with id=AA1, first strand: chain 'R' and resid 83 through 87 removed outlier: 3.507A pdb=" N GLN R 86 " --> pdb=" O VAL R 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 113 through 114 199 hydrogen bonds defined for protein. 591 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: 0.92 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1162 1.34 - 1.46: 1033 1.46 - 1.58: 1681 1.58 - 1.70: 0 1.70 - 1.81: 42 Bond restraints: 3918 Sorted by residual: bond pdb=" C TYR E 120 " pdb=" N PRO E 121 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.13e+00 bond pdb=" CA MET R 253 " pdb=" C MET R 253 " ideal model delta sigma weight residual 1.524 1.506 0.018 1.29e-02 6.01e+03 1.85e+00 bond pdb=" N LEU R 252 " pdb=" CA LEU R 252 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.42e+00 bond pdb=" CA TRP R 254 " pdb=" C TRP R 254 " ideal model delta sigma weight residual 1.523 1.509 0.015 1.30e-02 5.92e+03 1.28e+00 bond pdb=" N ARG R 173 " pdb=" CA ARG R 173 " ideal model delta sigma weight residual 1.459 1.445 0.014 1.21e-02 6.83e+03 1.27e+00 ... (remaining 3913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 5149 1.45 - 2.90: 145 2.90 - 4.34: 22 4.34 - 5.79: 15 5.79 - 7.24: 3 Bond angle restraints: 5334 Sorted by residual: angle pdb=" N ALA R 247 " pdb=" CA ALA R 247 " pdb=" C ALA R 247 " ideal model delta sigma weight residual 110.10 103.85 6.25 1.49e+00 4.50e-01 1.76e+01 angle pdb=" N MET R 253 " pdb=" CA MET R 253 " pdb=" C MET R 253 " ideal model delta sigma weight residual 111.36 107.96 3.40 1.09e+00 8.42e-01 9.72e+00 angle pdb=" N LYS R 249 " pdb=" CA LYS R 249 " pdb=" C LYS R 249 " ideal model delta sigma weight residual 108.90 113.91 -5.01 1.63e+00 3.76e-01 9.44e+00 angle pdb=" N LEU R 252 " pdb=" CA LEU R 252 " pdb=" C LEU R 252 " ideal model delta sigma weight residual 110.80 116.79 -5.99 2.13e+00 2.20e-01 7.91e+00 angle pdb=" C GLU R 248 " pdb=" N LYS R 249 " pdb=" CA LYS R 249 " ideal model delta sigma weight residual 122.99 119.22 3.77 1.41e+00 5.03e-01 7.16e+00 ... (remaining 5329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 2015 17.76 - 35.52: 205 35.52 - 53.28: 36 53.28 - 71.04: 5 71.04 - 88.80: 3 Dihedral angle restraints: 2264 sinusoidal: 891 harmonic: 1373 Sorted by residual: dihedral pdb=" CB CYS R 212 " pdb=" SG CYS R 212 " pdb=" SG CYS R 282 " pdb=" CB CYS R 282 " ideal model delta sinusoidal sigma weight residual 93.00 43.74 49.26 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 52.64 40.36 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -121.81 35.81 1 1.00e+01 1.00e-02 1.81e+01 ... (remaining 2261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 563 0.077 - 0.153: 30 0.153 - 0.230: 4 0.230 - 0.307: 1 0.307 - 0.383: 1 Chirality restraints: 599 Sorted by residual: chirality pdb=" CA PHE R 246 " pdb=" N PHE R 246 " pdb=" C PHE R 246 " pdb=" CB PHE R 246 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA LEU R 252 " pdb=" N LEU R 252 " pdb=" C LEU R 252 " pdb=" CB LEU R 252 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA GLU R 248 " pdb=" N GLU R 248 " pdb=" C GLU R 248 " pdb=" CB GLU R 248 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.32e-01 ... (remaining 596 not shown) Planarity restraints: 653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 96 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO R 97 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO R 97 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO R 97 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 296 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.62e+00 pdb=" N PRO R 297 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO R 297 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 297 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 96 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C ASP R 96 " 0.020 2.00e-02 2.50e+03 pdb=" O ASP R 96 " -0.007 2.00e-02 2.50e+03 pdb=" N PRO R 97 " -0.007 2.00e-02 2.50e+03 ... (remaining 650 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 72 2.69 - 3.24: 4048 3.24 - 3.80: 6093 3.80 - 4.35: 8134 4.35 - 4.90: 12421 Nonbonded interactions: 30768 Sorted by model distance: nonbonded pdb=" OG SER R 285 " pdb=" OD1 ASP R 287 " model vdw 2.141 3.040 nonbonded pdb=" O GLY E 33 " pdb=" NH1 ARG E 37 " model vdw 2.197 3.120 nonbonded pdb=" O SER R 170 " pdb=" OG SER R 170 " model vdw 2.296 3.040 nonbonded pdb=" OG SER R 155 " pdb=" OG SER R 381 " model vdw 2.319 3.040 nonbonded pdb=" OE2 GLU E 29 " pdb=" ND2 ASN E 31 " model vdw 2.352 3.120 ... (remaining 30763 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.560 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 0.038 3924 Z= 0.154 Angle : 0.643 7.242 5346 Z= 0.371 Chirality : 0.045 0.383 599 Planarity : 0.005 0.110 653 Dihedral : 14.107 88.802 1356 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.39), residues: 453 helix: -0.62 (0.30), residues: 298 sheet: -1.73 (1.17), residues: 12 loop : -1.67 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 69 HIS 0.003 0.001 HIS R 114 PHE 0.007 0.001 PHE R 384 TYR 0.005 0.001 TYR R 365 ARG 0.007 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.28911 ( 199) hydrogen bonds : angle 8.60424 ( 591) SS BOND : bond 0.00124 ( 6) SS BOND : angle 0.54485 ( 12) covalent geometry : bond 0.00269 ( 3918) covalent geometry : angle 0.64295 ( 5334) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: E 76 MET cc_start: 0.8313 (mpp) cc_final: 0.7857 (mpp) REVERT: R 100 LYS cc_start: 0.8536 (mmtm) cc_final: 0.8254 (mmtm) REVERT: R 248 GLU cc_start: 0.8119 (tp30) cc_final: 0.7903 (tm-30) REVERT: R 264 LEU cc_start: 0.8941 (tp) cc_final: 0.8640 (tp) REVERT: R 369 MET cc_start: 0.8294 (mmm) cc_final: 0.7986 (mmp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1812 time to fit residues: 15.9632 Evaluate side-chains 44 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 HIS R 219 HIS R 250 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.091679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.074063 restraints weight = 15474.809| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 4.67 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3924 Z= 0.180 Angle : 0.635 5.801 5346 Z= 0.335 Chirality : 0.041 0.132 599 Planarity : 0.005 0.081 653 Dihedral : 4.572 15.527 503 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.45 % Allowed : 8.67 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.39), residues: 453 helix: -0.22 (0.30), residues: 305 sheet: -1.46 (1.24), residues: 12 loop : -1.88 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 254 HIS 0.009 0.001 HIS R 295 PHE 0.013 0.001 PHE E 44 TYR 0.010 0.001 TYR E 66 ARG 0.004 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.05792 ( 199) hydrogen bonds : angle 5.22287 ( 591) SS BOND : bond 0.00206 ( 6) SS BOND : angle 0.88468 ( 12) covalent geometry : bond 0.00391 ( 3918) covalent geometry : angle 0.63433 ( 5334) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: R 85 MET cc_start: 0.9015 (tpp) cc_final: 0.8656 (tpp) REVERT: R 248 GLU cc_start: 0.8119 (tp30) cc_final: 0.7772 (tm-30) outliers start: 6 outliers final: 5 residues processed: 56 average time/residue: 0.1391 time to fit residues: 10.0949 Evaluate side-chains 55 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 395 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 HIS ** R 305 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 = 0.3886 r_free = 0.3886 target = 0.092760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.075208 restraints weight = 15472.938| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 4.70 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3924 Z= 0.143 Angle : 0.590 5.660 5346 Z= 0.304 Chirality : 0.040 0.235 599 Planarity : 0.004 0.069 653 Dihedral : 4.591 15.711 503 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.69 % Allowed : 11.81 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.40), residues: 453 helix: 0.04 (0.31), residues: 304 sheet: -0.97 (1.26), residues: 12 loop : -1.91 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 229 HIS 0.008 0.001 HIS R 295 PHE 0.009 0.001 PHE R 349 TYR 0.007 0.001 TYR R 227 ARG 0.003 0.000 ARG R 173 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 199) hydrogen bonds : angle 4.68490 ( 591) SS BOND : bond 0.00221 ( 6) SS BOND : angle 0.76475 ( 12) covalent geometry : bond 0.00318 ( 3918) covalent geometry : angle 0.58914 ( 5334) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: R 85 MET cc_start: 0.8818 (tpp) cc_final: 0.8615 (tpp) REVERT: R 248 GLU cc_start: 0.8208 (tp30) cc_final: 0.7753 (tm-30) REVERT: R 262 PHE cc_start: 0.8736 (t80) cc_final: 0.8503 (t80) outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 0.1582 time to fit residues: 12.5957 Evaluate side-chains 54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 395 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 305 ASN ** 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 = 0.3885 r_free = 0.3885 target = 0.092357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.074948 restraints weight = 15303.934| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 4.74 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3924 Z= 0.127 Angle : 0.585 6.082 5346 Z= 0.297 Chirality : 0.040 0.201 599 Planarity : 0.004 0.060 653 Dihedral : 4.556 14.283 503 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.69 % Allowed : 15.66 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.39), residues: 453 helix: 0.20 (0.31), residues: 294 sheet: -0.35 (1.42), residues: 12 loop : -1.86 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 254 HIS 0.007 0.001 HIS R 295 PHE 0.005 0.001 PHE R 349 TYR 0.007 0.001 TYR R 227 ARG 0.001 0.000 ARG R 119 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 199) hydrogen bonds : angle 4.45376 ( 591) SS BOND : bond 0.00205 ( 6) SS BOND : angle 0.75457 ( 12) covalent geometry : bond 0.00284 ( 3918) covalent geometry : angle 0.58449 ( 5334) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 223 MET cc_start: 0.8494 (mtt) cc_final: 0.8256 (mtt) REVERT: R 248 GLU cc_start: 0.8290 (tp30) cc_final: 0.7827 (tm-30) REVERT: R 262 PHE cc_start: 0.8737 (t80) cc_final: 0.8512 (t80) outliers start: 7 outliers final: 7 residues processed: 56 average time/residue: 0.1358 time to fit residues: 10.0178 Evaluate side-chains 58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 395 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 305 ASN ** 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 = 0.3929 r_free = 0.3929 target = 0.093139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.075664 restraints weight = 15601.679| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 4.63 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3924 Z= 0.133 Angle : 0.589 7.055 5346 Z= 0.295 Chirality : 0.039 0.194 599 Planarity : 0.004 0.054 653 Dihedral : 4.489 14.407 503 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.89 % Allowed : 17.11 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.40), residues: 453 helix: 0.32 (0.31), residues: 301 sheet: 0.14 (1.50), residues: 12 loop : -1.84 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 254 HIS 0.006 0.001 HIS R 295 PHE 0.006 0.001 PHE R 387 TYR 0.007 0.001 TYR R 227 ARG 0.003 0.000 ARG R 173 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 199) hydrogen bonds : angle 4.26534 ( 591) SS BOND : bond 0.00367 ( 6) SS BOND : angle 0.83281 ( 12) covalent geometry : bond 0.00304 ( 3918) covalent geometry : angle 0.58867 ( 5334) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 GLU cc_start: 0.8648 (mp0) cc_final: 0.8319 (mp0) REVERT: R 85 MET cc_start: 0.8964 (tpp) cc_final: 0.8628 (tpp) REVERT: R 223 MET cc_start: 0.8499 (mtt) cc_final: 0.8293 (mtm) REVERT: R 248 GLU cc_start: 0.8295 (tp30) cc_final: 0.7897 (tm-30) REVERT: R 262 PHE cc_start: 0.8735 (t80) cc_final: 0.8499 (t80) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.1261 time to fit residues: 10.8088 Evaluate side-chains 62 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 395 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 305 ASN ** 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 = 0.3883 r_free = 0.3883 target = 0.092534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.075384 restraints weight = 15542.893| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 4.71 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3924 Z= 0.128 Angle : 0.584 7.311 5346 Z= 0.295 Chirality : 0.040 0.208 599 Planarity : 0.004 0.049 653 Dihedral : 4.501 14.344 503 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.17 % Allowed : 17.59 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.41), residues: 453 helix: 0.44 (0.31), residues: 300 sheet: 0.18 (1.49), residues: 12 loop : -1.84 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 254 HIS 0.007 0.001 HIS R 295 PHE 0.005 0.001 PHE R 349 TYR 0.014 0.001 TYR R 277 ARG 0.003 0.000 ARG R 173 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 199) hydrogen bonds : angle 4.23701 ( 591) SS BOND : bond 0.00217 ( 6) SS BOND : angle 0.86499 ( 12) covalent geometry : bond 0.00290 ( 3918) covalent geometry : angle 0.58370 ( 5334) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 GLU cc_start: 0.8697 (mp0) cc_final: 0.8383 (mp0) REVERT: R 85 MET cc_start: 0.8756 (tpp) cc_final: 0.8513 (tpp) REVERT: R 248 GLU cc_start: 0.8323 (tp30) cc_final: 0.7851 (tm-30) REVERT: R 262 PHE cc_start: 0.8791 (t80) cc_final: 0.8529 (t80) REVERT: R 372 LEU cc_start: 0.9415 (mt) cc_final: 0.9206 (mp) outliers start: 9 outliers final: 8 residues processed: 64 average time/residue: 0.1766 time to fit residues: 15.0665 Evaluate side-chains 64 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 395 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 0.0770 chunk 42 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 305 ASN ** 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 = 0.3946 r_free = 0.3946 target = 0.093251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.075987 restraints weight = 15135.005| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 4.55 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3924 Z= 0.122 Angle : 0.598 6.412 5346 Z= 0.302 Chirality : 0.039 0.146 599 Planarity : 0.004 0.047 653 Dihedral : 4.460 14.632 503 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.69 % Allowed : 19.52 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.41), residues: 453 helix: 0.47 (0.31), residues: 301 sheet: 0.35 (1.52), residues: 12 loop : -1.77 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 229 HIS 0.008 0.001 HIS R 219 PHE 0.005 0.001 PHE R 349 TYR 0.007 0.001 TYR R 277 ARG 0.003 0.000 ARG R 173 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 199) hydrogen bonds : angle 4.13549 ( 591) SS BOND : bond 0.00244 ( 6) SS BOND : angle 1.15031 ( 12) covalent geometry : bond 0.00276 ( 3918) covalent geometry : angle 0.59609 ( 5334) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 GLU cc_start: 0.8714 (mp0) cc_final: 0.8393 (mp0) REVERT: R 85 MET cc_start: 0.8720 (tpp) cc_final: 0.8517 (tpp) REVERT: R 248 GLU cc_start: 0.8317 (tp30) cc_final: 0.7859 (tm-30) REVERT: R 262 PHE cc_start: 0.8775 (t80) cc_final: 0.8516 (t80) REVERT: R 268 CYS cc_start: 0.9077 (t) cc_final: 0.8809 (p) REVERT: R 349 PHE cc_start: 0.8663 (m-80) cc_final: 0.8420 (m-80) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.1534 time to fit residues: 13.0866 Evaluate side-chains 60 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 395 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 8 optimal weight: 0.0030 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 305 ASN ** 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 = 0.3907 r_free = 0.3907 target = 0.093513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.076495 restraints weight = 15380.808| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 4.81 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3924 Z= 0.122 Angle : 0.643 13.239 5346 Z= 0.312 Chirality : 0.043 0.389 599 Planarity : 0.004 0.047 653 Dihedral : 4.372 13.473 503 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.93 % Allowed : 20.96 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.40), residues: 453 helix: 0.52 (0.31), residues: 296 sheet: 0.46 (1.53), residues: 12 loop : -1.86 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 229 HIS 0.002 0.001 HIS E 97 PHE 0.006 0.001 PHE R 228 TYR 0.007 0.001 TYR R 227 ARG 0.001 0.000 ARG R 173 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 199) hydrogen bonds : angle 4.15750 ( 591) SS BOND : bond 0.00189 ( 6) SS BOND : angle 0.97348 ( 12) covalent geometry : bond 0.00280 ( 3918) covalent geometry : angle 0.64196 ( 5334) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 GLU cc_start: 0.8726 (mp0) cc_final: 0.8372 (mp0) REVERT: R 85 MET cc_start: 0.8682 (tpp) cc_final: 0.8477 (tpp) REVERT: R 223 MET cc_start: 0.8411 (mtt) cc_final: 0.8072 (mtm) REVERT: R 248 GLU cc_start: 0.8301 (tp30) cc_final: 0.7813 (tm-30) REVERT: R 262 PHE cc_start: 0.8808 (t80) cc_final: 0.8597 (t80) REVERT: R 268 CYS cc_start: 0.9098 (t) cc_final: 0.8804 (p) REVERT: R 349 PHE cc_start: 0.8627 (m-80) cc_final: 0.8384 (m-80) outliers start: 8 outliers final: 6 residues processed: 66 average time/residue: 0.2238 time to fit residues: 19.6857 Evaluate side-chains 61 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 30.0000 chunk 23 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 0.1980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN ** R 305 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 = 0.3901 r_free = 0.3901 target = 0.092559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.075407 restraints weight = 15342.887| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 4.77 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3924 Z= 0.134 Angle : 0.653 11.717 5346 Z= 0.319 Chirality : 0.041 0.255 599 Planarity : 0.004 0.046 653 Dihedral : 4.451 17.318 503 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.45 % Allowed : 21.45 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.40), residues: 453 helix: 0.45 (0.31), residues: 299 sheet: 0.52 (1.57), residues: 12 loop : -1.78 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 229 HIS 0.005 0.001 HIS E 97 PHE 0.006 0.001 PHE R 228 TYR 0.007 0.001 TYR R 365 ARG 0.001 0.000 ARG R 173 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 199) hydrogen bonds : angle 4.13816 ( 591) SS BOND : bond 0.00251 ( 6) SS BOND : angle 0.89088 ( 12) covalent geometry : bond 0.00312 ( 3918) covalent geometry : angle 0.65231 ( 5334) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 GLU cc_start: 0.8718 (mp0) cc_final: 0.8362 (mp0) REVERT: R 85 MET cc_start: 0.8574 (tpp) cc_final: 0.8351 (tpp) REVERT: R 223 MET cc_start: 0.8470 (mtt) cc_final: 0.8150 (mtm) REVERT: R 248 GLU cc_start: 0.8355 (tp30) cc_final: 0.7853 (tm-30) REVERT: R 262 PHE cc_start: 0.8814 (t80) cc_final: 0.8581 (t80) REVERT: R 268 CYS cc_start: 0.9073 (t) cc_final: 0.8782 (p) outliers start: 6 outliers final: 6 residues processed: 60 average time/residue: 0.2584 time to fit residues: 19.8134 Evaluate side-chains 60 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 305 ASN ** 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 = 0.3907 r_free = 0.3907 target = 0.093359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.076107 restraints weight = 15542.436| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 4.82 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3924 Z= 0.131 Angle : 0.653 10.763 5346 Z= 0.319 Chirality : 0.041 0.226 599 Planarity : 0.004 0.049 653 Dihedral : 4.433 17.788 503 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.20 % Allowed : 22.17 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.41), residues: 453 helix: 0.51 (0.31), residues: 302 sheet: 0.70 (1.67), residues: 12 loop : -1.78 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 72 HIS 0.004 0.001 HIS R 370 PHE 0.007 0.001 PHE R 387 TYR 0.008 0.001 TYR R 365 ARG 0.002 0.000 ARG R 173 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 199) hydrogen bonds : angle 4.10672 ( 591) SS BOND : bond 0.00208 ( 6) SS BOND : angle 0.79601 ( 12) covalent geometry : bond 0.00303 ( 3918) covalent geometry : angle 0.65270 ( 5334) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 GLU cc_start: 0.8713 (mp0) cc_final: 0.8353 (mp0) REVERT: R 85 MET cc_start: 0.8512 (tpp) cc_final: 0.8293 (tpp) REVERT: R 90 ASP cc_start: 0.9290 (p0) cc_final: 0.8885 (m-30) REVERT: R 223 MET cc_start: 0.8481 (mtt) cc_final: 0.8169 (mtm) REVERT: R 248 GLU cc_start: 0.8348 (tp30) cc_final: 0.7857 (tm-30) REVERT: R 262 PHE cc_start: 0.8813 (t80) cc_final: 0.8584 (t80) REVERT: R 268 CYS cc_start: 0.9065 (t) cc_final: 0.8774 (p) outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 0.2116 time to fit residues: 16.1160 Evaluate side-chains 59 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.0570 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 305 ASN ** 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 = 0.3914 r_free = 0.3914 target = 0.093301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.076184 restraints weight = 15218.336| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 4.77 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3924 Z= 0.125 Angle : 0.635 9.235 5346 Z= 0.311 Chirality : 0.040 0.200 599 Planarity : 0.004 0.051 653 Dihedral : 4.401 18.846 503 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.20 % Allowed : 21.93 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.41), residues: 453 helix: 0.51 (0.31), residues: 303 sheet: 0.67 (1.67), residues: 12 loop : -1.71 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 72 HIS 0.003 0.001 HIS E 97 PHE 0.005 0.001 PHE E 93 TYR 0.007 0.001 TYR R 365 ARG 0.002 0.000 ARG R 173 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 199) hydrogen bonds : angle 4.06296 ( 591) SS BOND : bond 0.00219 ( 6) SS BOND : angle 0.76225 ( 12) covalent geometry : bond 0.00290 ( 3918) covalent geometry : angle 0.63507 ( 5334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1991.92 seconds wall clock time: 36 minutes 53.08 seconds (2213.08 seconds total)